Multiple sequence alignment - TraesCS5D01G422300

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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 TraesCS5D01G422300 chr5D 100.000 9395 0 0 488 9882 482291584 482300978 0.000000e+00 17350.0
1 TraesCS5D01G422300 chr5D 90.473 1396 114 9 7644 9027 480480953 480479565 0.000000e+00 1823.0
2 TraesCS5D01G422300 chr5D 90.488 1230 115 2 1701 2930 482562950 482564177 0.000000e+00 1622.0
3 TraesCS5D01G422300 chr5D 88.636 484 54 1 6754 7237 482246567 482247049 1.110000e-163 588.0
4 TraesCS5D01G422300 chr5D 84.286 420 32 14 9395 9784 480479172 480478757 7.240000e-101 379.0
5 TraesCS5D01G422300 chr5D 89.076 238 24 2 7000 7237 482412334 482412569 2.700000e-75 294.0
6 TraesCS5D01G422300 chr5D 82.201 309 44 5 7296 7599 482555859 482556161 1.270000e-63 255.0
7 TraesCS5D01G422300 chr5D 80.057 351 59 8 3863 4203 482552358 482552707 5.930000e-62 250.0
8 TraesCS5D01G422300 chr5D 79.822 337 55 9 3868 4192 482245657 482245992 5.970000e-57 233.0
9 TraesCS5D01G422300 chr5D 79.882 338 43 9 7300 7619 482412601 482412931 3.590000e-54 224.0
10 TraesCS5D01G422300 chr5D 100.000 108 0 0 1 108 482291097 482291204 6.050000e-47 200.0
11 TraesCS5D01G422300 chr5D 84.234 222 15 7 9099 9300 480479438 480479217 2.180000e-46 198.0
12 TraesCS5D01G422300 chr5D 83.060 183 25 3 998 1174 482562381 482562563 2.860000e-35 161.0
13 TraesCS5D01G422300 chr5D 90.588 85 8 0 3351 3435 482589114 482589198 8.110000e-21 113.0
14 TraesCS5D01G422300 chr5D 82.482 137 14 8 3370 3505 482410726 482410853 2.920000e-20 111.0
15 TraesCS5D01G422300 chr5D 89.412 85 9 0 3351 3435 482245012 482245096 3.770000e-19 108.0
16 TraesCS5D01G422300 chr5D 80.822 146 10 8 1191 1319 482562641 482562785 2.270000e-16 99.0
17 TraesCS5D01G422300 chr5D 100.000 35 0 0 7316 7350 482247076 482247110 2.300000e-06 65.8
18 TraesCS5D01G422300 chr5B 96.030 3426 95 20 4277 7687 591650160 591653559 0.000000e+00 5535.0
19 TraesCS5D01G422300 chr5B 98.840 2758 29 3 1457 4213 591647407 591650162 0.000000e+00 4913.0
20 TraesCS5D01G422300 chr5B 91.722 1812 93 22 7719 9500 591653553 591655337 0.000000e+00 2462.0
21 TraesCS5D01G422300 chr5B 90.694 1397 113 7 7644 9029 588683399 588682009 0.000000e+00 1844.0
22 TraesCS5D01G422300 chr5B 90.325 1230 117 2 1701 2930 591816410 591817637 0.000000e+00 1611.0
23 TraesCS5D01G422300 chr5B 92.653 490 30 5 677 1161 591646859 591647347 0.000000e+00 701.0
24 TraesCS5D01G422300 chr5B 83.773 721 84 21 4641 5342 108166897 108166191 0.000000e+00 652.0
25 TraesCS5D01G422300 chr5B 88.017 484 57 1 6754 7237 591556433 591556915 1.110000e-158 571.0
26 TraesCS5D01G422300 chr5B 91.005 378 22 4 9508 9882 591655447 591655815 5.330000e-137 499.0
27 TraesCS5D01G422300 chr5B 88.323 334 29 3 488 819 591646535 591646860 9.300000e-105 392.0
28 TraesCS5D01G422300 chr5B 79.037 353 63 8 3861 4203 591782419 591782770 2.150000e-56 231.0
29 TraesCS5D01G422300 chr5B 78.006 341 46 21 7318 7643 591638909 591639235 4.710000e-43 187.0
30 TraesCS5D01G422300 chr5B 76.316 380 66 17 3349 3723 591781746 591782106 2.190000e-41 182.0
31 TraesCS5D01G422300 chr5B 90.226 133 11 1 9099 9229 588681875 588681743 1.320000e-38 172.0
32 TraesCS5D01G422300 chr5B 95.370 108 5 0 1 108 591646329 591646436 1.320000e-38 172.0
33 TraesCS5D01G422300 chr5B 84.153 183 23 3 998 1174 591814359 591814541 1.320000e-38 172.0
34 TraesCS5D01G422300 chr5B 90.588 85 8 0 3351 3435 591829196 591829280 8.110000e-21 113.0
35 TraesCS5D01G422300 chr5B 88.235 85 10 0 3351 3435 591554932 591555016 1.760000e-17 102.0
36 TraesCS5D01G422300 chr5B 94.737 57 1 2 1603 1659 440023160 440023214 4.920000e-13 87.9
37 TraesCS5D01G422300 chr5B 97.143 35 1 0 7316 7350 591556941 591556975 1.070000e-04 60.2
38 TraesCS5D01G422300 chr5A 97.202 1894 51 2 1456 3348 601993083 601994975 0.000000e+00 3203.0
39 TraesCS5D01G422300 chr5A 92.804 1598 97 13 7639 9229 602003638 602005224 0.000000e+00 2298.0
40 TraesCS5D01G422300 chr5A 90.294 1463 118 10 7644 9095 599223819 599222370 0.000000e+00 1893.0
41 TraesCS5D01G422300 chr5A 90.881 1294 101 10 5840 7122 601996732 601998019 0.000000e+00 1720.0
42 TraesCS5D01G422300 chr5A 91.379 928 56 10 3346 4272 601995327 601996231 0.000000e+00 1249.0
43 TraesCS5D01G422300 chr5A 98.750 320 4 0 845 1164 601992092 601992411 4.000000e-158 569.0
44 TraesCS5D01G422300 chr5A 87.397 484 57 4 6754 7237 601729262 601729741 4.030000e-153 553.0
45 TraesCS5D01G422300 chr5A 83.087 609 72 19 5187 5768 619482853 619482249 8.790000e-145 525.0
46 TraesCS5D01G422300 chr5A 81.120 625 79 23 6643 7257 602334147 602334742 1.940000e-126 464.0
47 TraesCS5D01G422300 chr5A 94.700 283 10 3 1169 1446 601992492 601992774 1.520000e-117 435.0
48 TraesCS5D01G422300 chr5A 97.872 235 5 0 7409 7643 601998208 601998442 3.320000e-109 407.0
49 TraesCS5D01G422300 chr5A 90.417 240 21 2 4408 4646 554065904 554065666 2.070000e-81 315.0
50 TraesCS5D01G422300 chr5A 90.041 241 21 3 4408 4646 619483805 619483566 9.640000e-80 309.0
51 TraesCS5D01G422300 chr5A 90.295 237 21 2 4408 4643 666686766 666687001 9.640000e-80 309.0
52 TraesCS5D01G422300 chr5A 87.755 245 10 8 9544 9788 602045167 602045391 1.640000e-67 268.0
53 TraesCS5D01G422300 chr5A 82.848 309 42 5 7298 7601 602334727 602335029 5.880000e-67 267.0
54 TraesCS5D01G422300 chr5A 90.777 206 8 5 531 733 601991902 601992099 2.120000e-66 265.0
55 TraesCS5D01G422300 chr5A 82.079 279 35 9 3991 4267 602332833 602333098 3.590000e-54 224.0
56 TraesCS5D01G422300 chr5A 89.773 176 17 1 663 838 653299427 653299601 3.590000e-54 224.0
57 TraesCS5D01G422300 chr5A 85.520 221 14 10 9099 9301 599222266 599222046 2.160000e-51 215.0
58 TraesCS5D01G422300 chr5A 93.023 129 7 2 7147 7274 601998015 601998142 4.710000e-43 187.0
59 TraesCS5D01G422300 chr5A 90.840 131 12 0 4267 4397 616085824 616085954 1.020000e-39 176.0
60 TraesCS5D01G422300 chr5A 90.152 132 13 0 4266 4397 30810644 30810775 1.320000e-38 172.0
61 TraesCS5D01G422300 chr5A 88.652 141 13 3 4259 4397 619482244 619482383 1.710000e-37 169.0
62 TraesCS5D01G422300 chr5A 96.875 96 3 0 5758 5853 601996223 601996318 2.860000e-35 161.0
63 TraesCS5D01G422300 chr5A 90.816 98 2 1 1 98 601991746 601991836 3.750000e-24 124.0
64 TraesCS5D01G422300 chr5A 93.421 76 5 0 7298 7373 601998124 601998199 8.110000e-21 113.0
65 TraesCS5D01G422300 chr5A 90.000 90 2 4 9394 9476 599221987 599221898 1.050000e-19 110.0
66 TraesCS5D01G422300 chr5A 74.041 339 55 21 3351 3683 601727795 601728106 3.770000e-19 108.0
67 TraesCS5D01G422300 chr5A 97.143 35 1 0 7316 7350 601729769 601729803 1.070000e-04 60.2
68 TraesCS5D01G422300 chr7D 85.203 838 118 5 2107 2940 598027582 598026747 0.000000e+00 856.0
69 TraesCS5D01G422300 chr7D 85.049 816 116 4 2105 2919 597343761 597344571 0.000000e+00 826.0
70 TraesCS5D01G422300 chr7D 83.914 833 121 11 2106 2930 597474916 597474089 0.000000e+00 784.0
71 TraesCS5D01G422300 chr7D 84.000 450 63 4 1644 2085 597343326 597343774 3.300000e-114 424.0
72 TraesCS5D01G422300 chr7D 81.596 451 72 8 1645 2094 597475335 597474895 7.300000e-96 363.0
73 TraesCS5D01G422300 chr7D 84.830 323 43 6 1763 2082 598027893 598027574 4.450000e-83 320.0
74 TraesCS5D01G422300 chr7D 90.230 174 17 0 677 850 566026575 566026748 2.780000e-55 228.0
75 TraesCS5D01G422300 chr2D 88.227 688 70 9 5079 5757 592992739 592993424 0.000000e+00 811.0
76 TraesCS5D01G422300 chr2D 87.069 696 82 3 5079 5767 44369950 44370644 0.000000e+00 780.0
77 TraesCS5D01G422300 chr2D 86.667 495 36 7 4406 4893 592992257 592992728 1.140000e-143 521.0
78 TraesCS5D01G422300 chr2D 86.061 495 38 8 4406 4893 44369469 44369939 4.120000e-138 503.0
79 TraesCS5D01G422300 chr2D 92.063 126 10 0 4272 4397 592992076 592992201 2.840000e-40 178.0
80 TraesCS5D01G422300 chr2D 88.489 139 15 1 4264 4401 556405951 556405813 6.140000e-37 167.0
81 TraesCS5D01G422300 chr4B 79.064 1175 231 11 7728 8892 538999091 538997922 0.000000e+00 793.0
82 TraesCS5D01G422300 chr4B 84.284 719 83 19 4641 5342 57976117 57976822 0.000000e+00 675.0
83 TraesCS5D01G422300 chr4D 78.979 1175 232 10 7728 8892 437028938 437027769 0.000000e+00 787.0
84 TraesCS5D01G422300 chr4D 90.698 172 16 0 675 846 34661525 34661696 7.720000e-56 230.0
85 TraesCS5D01G422300 chr4D 94.915 59 2 1 1600 1657 418584412 418584470 3.800000e-14 91.6
86 TraesCS5D01G422300 chrUn 87.249 698 74 7 5079 5765 269228661 269229354 0.000000e+00 782.0
87 TraesCS5D01G422300 chrUn 83.866 719 86 19 4641 5342 316819336 316820041 0.000000e+00 658.0
88 TraesCS5D01G422300 chrUn 83.866 719 86 19 4641 5342 328625621 328624916 0.000000e+00 658.0
89 TraesCS5D01G422300 chrUn 88.153 498 41 7 4406 4896 269228167 269228653 2.390000e-160 577.0
90 TraesCS5D01G422300 chrUn 85.857 502 39 11 4406 4900 349248639 349249115 1.150000e-138 505.0
91 TraesCS5D01G422300 chrUn 85.657 502 40 11 4406 4900 339475419 339475895 5.330000e-137 499.0
92 TraesCS5D01G422300 chrUn 86.294 197 21 6 645 838 178663491 178663684 1.010000e-49 209.0
93 TraesCS5D01G422300 chr1D 87.249 698 74 7 5079 5765 3098427 3099120 0.000000e+00 782.0
94 TraesCS5D01G422300 chr1D 88.153 498 41 7 4406 4896 3097933 3098419 2.390000e-160 577.0
95 TraesCS5D01G422300 chr1D 87.069 464 54 6 5301 5761 296938304 296938764 4.090000e-143 520.0
96 TraesCS5D01G422300 chr1D 94.828 58 0 2 1599 1656 59867984 59868038 4.920000e-13 87.9
97 TraesCS5D01G422300 chr7B 83.293 826 128 8 2105 2923 677073387 677074209 0.000000e+00 752.0
98 TraesCS5D01G422300 chr7B 82.878 841 112 15 2105 2919 675996954 675997788 0.000000e+00 726.0
99 TraesCS5D01G422300 chr7B 84.000 450 64 3 1644 2085 675996518 675996967 9.170000e-115 425.0
100 TraesCS5D01G422300 chr7B 90.295 237 21 2 4408 4643 450632846 450633081 9.640000e-80 309.0
101 TraesCS5D01G422300 chr7B 90.643 171 14 1 670 838 518918294 518918124 9.990000e-55 226.0
102 TraesCS5D01G422300 chr4A 78.450 1174 233 12 7728 8892 31414053 31415215 0.000000e+00 749.0
103 TraesCS5D01G422300 chr6B 84.145 719 84 19 4641 5342 694114119 694114824 0.000000e+00 669.0
104 TraesCS5D01G422300 chr6B 91.566 166 12 2 677 841 172738532 172738368 2.780000e-55 228.0
105 TraesCS5D01G422300 chr6B 96.429 56 2 0 1599 1654 48981476 48981421 1.060000e-14 93.5
106 TraesCS5D01G422300 chr3B 84.145 719 84 19 4641 5342 10933201 10932496 0.000000e+00 669.0
107 TraesCS5D01G422300 chr3B 83.764 271 41 2 6759 7029 821093328 821093061 4.580000e-63 254.0
108 TraesCS5D01G422300 chr3B 89.474 133 14 0 4265 4397 751196731 751196863 1.710000e-37 169.0
109 TraesCS5D01G422300 chr3A 83.866 719 86 19 4641 5342 55735830 55736535 0.000000e+00 658.0
110 TraesCS5D01G422300 chr3A 83.417 597 69 17 5187 5757 20443879 20444471 2.440000e-145 527.0
111 TraesCS5D01G422300 chr3A 90.717 237 20 2 4408 4643 20443133 20443368 2.070000e-81 315.0
112 TraesCS5D01G422300 chr3A 86.842 76 5 5 1601 1676 466807027 466807097 8.230000e-11 80.5
113 TraesCS5D01G422300 chr1B 83.866 719 86 19 4641 5342 560332397 560333102 0.000000e+00 658.0
114 TraesCS5D01G422300 chr1B 98.113 53 0 1 1601 1653 645568270 645568321 3.800000e-14 91.6
115 TraesCS5D01G422300 chr2B 80.695 834 131 16 1262 2085 765391715 765392528 1.090000e-173 621.0
116 TraesCS5D01G422300 chr2A 82.943 598 71 18 5187 5757 771536360 771535767 2.460000e-140 510.0
117 TraesCS5D01G422300 chr2A 90.417 240 21 2 4408 4646 771537106 771536868 2.070000e-81 315.0
118 TraesCS5D01G422300 chr2A 89.326 178 16 3 660 834 539327934 539328111 4.650000e-53 220.0
119 TraesCS5D01G422300 chr2A 88.079 151 12 5 4247 4397 676162713 676162569 3.670000e-39 174.0
120 TraesCS5D01G422300 chr1A 85.657 502 40 11 4406 4900 561738859 561739335 5.330000e-137 499.0
121 TraesCS5D01G422300 chr1A 87.624 404 41 6 4641 5042 8585687 8585291 2.510000e-125 460.0
122 TraesCS5D01G422300 chr1A 90.000 240 22 2 4408 4646 465087533 465087295 9.640000e-80 309.0
123 TraesCS5D01G422300 chr7A 90.417 240 21 2 4408 4646 566998845 566998607 2.070000e-81 315.0
124 TraesCS5D01G422300 chr7A 90.625 64 4 2 1601 1663 736667402 736667464 6.360000e-12 84.2
125 TraesCS5D01G422300 chr3D 91.228 171 12 3 670 839 482202483 482202315 7.720000e-56 230.0
126 TraesCS5D01G422300 chr3D 93.077 130 8 1 4269 4397 549741731 549741860 1.310000e-43 189.0


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 TraesCS5D01G422300 chr5D 482291097 482300978 9881 False 8775.000000 17350 100.000000 1 9882 2 chr5D.!!$F3 9881
1 TraesCS5D01G422300 chr5D 480478757 480480953 2196 True 800.000000 1823 86.331000 7644 9784 3 chr5D.!!$R1 2140
2 TraesCS5D01G422300 chr5D 482562381 482564177 1796 False 627.333333 1622 84.790000 998 2930 3 chr5D.!!$F6 1932
3 TraesCS5D01G422300 chr5D 482552358 482556161 3803 False 252.500000 255 81.129000 3863 7599 2 chr5D.!!$F5 3736
4 TraesCS5D01G422300 chr5D 482245012 482247110 2098 False 248.700000 588 89.467500 3351 7350 4 chr5D.!!$F2 3999
5 TraesCS5D01G422300 chr5D 482410726 482412931 2205 False 209.666667 294 83.813333 3370 7619 3 chr5D.!!$F4 4249
6 TraesCS5D01G422300 chr5B 591646329 591655815 9486 False 2096.285714 5535 93.420429 1 9882 7 chr5B.!!$F5 9881
7 TraesCS5D01G422300 chr5B 588681743 588683399 1656 True 1008.000000 1844 90.460000 7644 9229 2 chr5B.!!$R2 1585
8 TraesCS5D01G422300 chr5B 591814359 591817637 3278 False 891.500000 1611 87.239000 998 2930 2 chr5B.!!$F7 1932
9 TraesCS5D01G422300 chr5B 108166191 108166897 706 True 652.000000 652 83.773000 4641 5342 1 chr5B.!!$R1 701
10 TraesCS5D01G422300 chr5B 591554932 591556975 2043 False 244.400000 571 91.131667 3351 7350 3 chr5B.!!$F4 3999
11 TraesCS5D01G422300 chr5B 591781746 591782770 1024 False 206.500000 231 77.676500 3349 4203 2 chr5B.!!$F6 854
12 TraesCS5D01G422300 chr5A 602003638 602005224 1586 False 2298.000000 2298 92.804000 7639 9229 1 chr5A.!!$F2 1590
13 TraesCS5D01G422300 chr5A 601991746 601998442 6696 False 766.636364 3203 94.154182 1 7643 11 chr5A.!!$F9 7642
14 TraesCS5D01G422300 chr5A 599221898 599223819 1921 True 739.333333 1893 88.604667 7644 9476 3 chr5A.!!$R2 1832
15 TraesCS5D01G422300 chr5A 619482249 619483805 1556 True 417.000000 525 86.564000 4408 5768 2 chr5A.!!$R3 1360
16 TraesCS5D01G422300 chr5A 602332833 602335029 2196 False 318.333333 464 82.015667 3991 7601 3 chr5A.!!$F10 3610
17 TraesCS5D01G422300 chr5A 601727795 601729803 2008 False 240.400000 553 86.193667 3351 7350 3 chr5A.!!$F8 3999
18 TraesCS5D01G422300 chr7D 597343326 597344571 1245 False 625.000000 826 84.524500 1644 2919 2 chr7D.!!$F2 1275
19 TraesCS5D01G422300 chr7D 598026747 598027893 1146 True 588.000000 856 85.016500 1763 2940 2 chr7D.!!$R2 1177
20 TraesCS5D01G422300 chr7D 597474089 597475335 1246 True 573.500000 784 82.755000 1645 2930 2 chr7D.!!$R1 1285
21 TraesCS5D01G422300 chr2D 44369469 44370644 1175 False 641.500000 780 86.565000 4406 5767 2 chr2D.!!$F1 1361
22 TraesCS5D01G422300 chr2D 592992076 592993424 1348 False 503.333333 811 88.985667 4272 5757 3 chr2D.!!$F2 1485
23 TraesCS5D01G422300 chr4B 538997922 538999091 1169 True 793.000000 793 79.064000 7728 8892 1 chr4B.!!$R1 1164
24 TraesCS5D01G422300 chr4B 57976117 57976822 705 False 675.000000 675 84.284000 4641 5342 1 chr4B.!!$F1 701
25 TraesCS5D01G422300 chr4D 437027769 437028938 1169 True 787.000000 787 78.979000 7728 8892 1 chr4D.!!$R1 1164
26 TraesCS5D01G422300 chrUn 269228167 269229354 1187 False 679.500000 782 87.701000 4406 5765 2 chrUn.!!$F5 1359
27 TraesCS5D01G422300 chrUn 316819336 316820041 705 False 658.000000 658 83.866000 4641 5342 1 chrUn.!!$F2 701
28 TraesCS5D01G422300 chrUn 328624916 328625621 705 True 658.000000 658 83.866000 4641 5342 1 chrUn.!!$R1 701
29 TraesCS5D01G422300 chr1D 3097933 3099120 1187 False 679.500000 782 87.701000 4406 5765 2 chr1D.!!$F3 1359
30 TraesCS5D01G422300 chr7B 677073387 677074209 822 False 752.000000 752 83.293000 2105 2923 1 chr7B.!!$F2 818
31 TraesCS5D01G422300 chr7B 675996518 675997788 1270 False 575.500000 726 83.439000 1644 2919 2 chr7B.!!$F3 1275
32 TraesCS5D01G422300 chr4A 31414053 31415215 1162 False 749.000000 749 78.450000 7728 8892 1 chr4A.!!$F1 1164
33 TraesCS5D01G422300 chr6B 694114119 694114824 705 False 669.000000 669 84.145000 4641 5342 1 chr6B.!!$F1 701
34 TraesCS5D01G422300 chr3B 10932496 10933201 705 True 669.000000 669 84.145000 4641 5342 1 chr3B.!!$R1 701
35 TraesCS5D01G422300 chr3A 55735830 55736535 705 False 658.000000 658 83.866000 4641 5342 1 chr3A.!!$F1 701
36 TraesCS5D01G422300 chr3A 20443133 20444471 1338 False 421.000000 527 87.067000 4408 5757 2 chr3A.!!$F3 1349
37 TraesCS5D01G422300 chr1B 560332397 560333102 705 False 658.000000 658 83.866000 4641 5342 1 chr1B.!!$F1 701
38 TraesCS5D01G422300 chr2B 765391715 765392528 813 False 621.000000 621 80.695000 1262 2085 1 chr2B.!!$F1 823
39 TraesCS5D01G422300 chr2A 771535767 771537106 1339 True 412.500000 510 86.680000 4408 5757 2 chr2A.!!$R2 1349

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
632 641 0.388134 CTGTGTTACTGTCGGGTCCG 60.388 60.000 2.52 2.52 41.35 4.79 F
1579 3640 0.675837 GACCCCGGGAGTAAACTTGC 60.676 60.000 26.32 0.37 0.00 4.01 F
3054 5163 3.371595 GGCCCTTCCATACAAGCTAGAAA 60.372 47.826 0.00 0.00 34.01 2.52 F
4072 6951 4.445452 AAAGAAGAAGCGGTACATCGTA 57.555 40.909 0.00 0.00 0.00 3.43 F
5003 8161 0.544697 ATGTGGAATGGGGTACGACC 59.455 55.000 0.00 0.00 37.60 4.79 F
5152 8471 0.175760 CCTGATGGGGTCACGTACAG 59.824 60.000 0.00 0.00 32.22 2.74 F
5585 8931 1.644913 AAAAACCGTCGAAGTGGCG 59.355 52.632 0.00 0.00 0.00 5.69 F
7096 12638 1.069022 CGCAGTCCTGTCAAACAATGG 60.069 52.381 0.00 0.00 0.00 3.16 F
8155 13751 2.831333 ACTATCATTCAGGCTCTTGCG 58.169 47.619 0.00 0.00 40.82 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3055 5164 4.790937 TGTCTTTAGGATATTGCCATGCA 58.209 39.130 0.00 0.00 36.47 3.96 R
3072 5181 2.620115 CCTTGTTGTGCAGTCATGTCTT 59.380 45.455 0.00 0.00 0.00 3.01 R
4698 7627 0.107703 TTGTAAGGCGCAGAGATGGG 60.108 55.000 10.83 0.00 0.00 4.00 R
5102 8421 0.324943 TCTTCTTCCTCCTTTGGCGG 59.675 55.000 0.00 0.00 0.00 6.13 R
6480 11922 1.607148 GTGCTTGAAGGGGTGTAACAC 59.393 52.381 0.00 0.00 41.97 3.32 R
6521 12055 2.033550 CACTAGGGTTGTAGCTAGCTCG 59.966 54.545 23.26 2.32 0.00 5.03 R
7391 12958 3.532641 ATTTCCCTGGGGCAGATAATC 57.467 47.619 14.00 0.00 32.44 1.75 R
8278 13874 0.817634 TGAACTCAAAGGGCACACCG 60.818 55.000 0.00 0.00 46.96 4.94 R
9739 15625 0.322277 AGCTCCTGTTGCTGTCATGG 60.322 55.000 0.00 0.00 39.56 3.66 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
539 548 2.418884 GCCCTACTCAGGTTAGTGCTTC 60.419 54.545 0.00 0.00 40.79 3.86
630 639 1.669211 GCTCTGTGTTACTGTCGGGTC 60.669 57.143 0.00 0.00 0.00 4.46
631 640 0.963962 TCTGTGTTACTGTCGGGTCC 59.036 55.000 0.00 0.00 0.00 4.46
632 641 0.388134 CTGTGTTACTGTCGGGTCCG 60.388 60.000 2.52 2.52 41.35 4.79
633 642 1.735559 GTGTTACTGTCGGGTCCGC 60.736 63.158 4.27 0.99 39.59 5.54
634 643 2.201708 TGTTACTGTCGGGTCCGCA 61.202 57.895 4.27 5.56 39.59 5.69
635 644 1.735559 GTTACTGTCGGGTCCGCAC 60.736 63.158 4.27 5.01 39.59 5.34
636 645 1.904865 TTACTGTCGGGTCCGCACT 60.905 57.895 4.27 0.00 39.59 4.40
643 652 4.767255 GGGTCCGCACTCTGCAGG 62.767 72.222 15.13 7.28 45.36 4.85
734 745 9.751542 AGAGATTTCAATAAGAACTACGTATGG 57.248 33.333 0.00 0.00 35.56 2.74
735 746 9.745880 GAGATTTCAATAAGAACTACGTATGGA 57.254 33.333 0.00 0.00 35.56 3.41
785 796 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
791 802 5.105310 ACTCATTTTGCTCCGTATGTAGTCT 60.105 40.000 0.00 0.00 0.00 3.24
798 809 4.885325 TGCTCCGTATGTAGTCTGTATTGA 59.115 41.667 0.00 0.00 0.00 2.57
889 1044 5.823209 TGTGCAAGTTCCATTCATCTATG 57.177 39.130 0.00 0.00 0.00 2.23
949 1104 4.846940 AGGTCAATAAGGAGAAGGTGAGTT 59.153 41.667 0.00 0.00 0.00 3.01
1169 1330 8.437360 TCCTGACATCAACAATATCATACAAC 57.563 34.615 0.00 0.00 0.00 3.32
1177 1418 6.481976 TCAACAATATCATACAACCATCGTCC 59.518 38.462 0.00 0.00 0.00 4.79
1318 3076 3.565307 TCAGTTGAGCACAAGGGATTTT 58.435 40.909 0.00 0.00 36.64 1.82
1371 3130 1.227943 AGGCTTCAAGCTGCGTGAA 60.228 52.632 25.24 25.24 41.99 3.18
1579 3640 0.675837 GACCCCGGGAGTAAACTTGC 60.676 60.000 26.32 0.37 0.00 4.01
3054 5163 3.371595 GGCCCTTCCATACAAGCTAGAAA 60.372 47.826 0.00 0.00 34.01 2.52
3055 5164 4.464947 GCCCTTCCATACAAGCTAGAAAT 58.535 43.478 0.00 0.00 0.00 2.17
3072 5181 6.151648 GCTAGAAATGCATGGCAATATCCTAA 59.848 38.462 0.00 0.00 43.62 2.69
3896 6765 7.840931 AGGTCGTAGATCATTAATATGCATGA 58.159 34.615 10.16 0.00 42.44 3.07
3988 6858 7.597369 CGGTATCGTAATGAACAGATTCCATAA 59.403 37.037 0.00 0.00 32.93 1.90
4072 6951 4.445452 AAAGAAGAAGCGGTACATCGTA 57.555 40.909 0.00 0.00 0.00 3.43
4167 7046 6.203723 GCTTTATGGGTCATTATCACAGAGAC 59.796 42.308 0.00 0.00 0.00 3.36
4325 7205 7.222000 TGACATTTTTGACACTAATTACCCC 57.778 36.000 0.00 0.00 0.00 4.95
4371 7251 6.487299 TTACCCCATTTAGCAAAAGTGTTT 57.513 33.333 0.00 0.00 0.00 2.83
4698 7627 6.696411 TGTCACAAACCATAAAAATCATCCC 58.304 36.000 0.00 0.00 0.00 3.85
5003 8161 0.544697 ATGTGGAATGGGGTACGACC 59.455 55.000 0.00 0.00 37.60 4.79
5102 8421 0.183492 TGATGGGGTCCTTGCTATGC 59.817 55.000 0.00 0.00 0.00 3.14
5152 8471 0.175760 CCTGATGGGGTCACGTACAG 59.824 60.000 0.00 0.00 32.22 2.74
5585 8931 1.644913 AAAAACCGTCGAAGTGGCG 59.355 52.632 0.00 0.00 0.00 5.69
5787 9134 3.483869 GCCCAGTGCCTCCTAGGG 61.484 72.222 9.46 0.00 42.55 3.53
5905 9691 2.237392 ACTTACTGGCATGAAGGAGGAC 59.763 50.000 11.79 0.00 0.00 3.85
5906 9692 2.254152 TACTGGCATGAAGGAGGACT 57.746 50.000 0.00 0.00 0.00 3.85
6117 9914 6.204852 TCCATGTCCATCATAATTAGGCTT 57.795 37.500 0.00 0.00 34.67 4.35
6479 11921 8.876275 TTCCTATAAGCGTATGATAAAAACGT 57.124 30.769 2.09 0.00 38.81 3.99
6480 11922 8.289440 TCCTATAAGCGTATGATAAAAACGTG 57.711 34.615 2.09 0.00 38.81 4.49
6521 12055 5.222631 CACAGTAGAATTCAACAAAAGGGC 58.777 41.667 8.44 0.00 0.00 5.19
6543 12077 3.288964 GAGCTAGCTACAACCCTAGTGA 58.711 50.000 19.38 0.00 34.81 3.41
6626 12161 1.921982 TGCTGGCACCAATACATTGT 58.078 45.000 0.00 0.00 36.06 2.71
6703 12243 1.482954 TAGATGCTCTGCTGCAGTCT 58.517 50.000 27.24 23.15 46.71 3.24
6927 12469 6.097129 GGTCCTTCTGTACAAGCTAGAACTAT 59.903 42.308 0.00 0.00 0.00 2.12
6972 12514 1.516453 CGCACAACACGGTGATTTTTG 59.484 47.619 16.29 11.05 41.32 2.44
7025 12567 8.565896 TGCACTACATGTTTCTCTAAATTCAT 57.434 30.769 2.30 0.00 0.00 2.57
7096 12638 1.069022 CGCAGTCCTGTCAAACAATGG 60.069 52.381 0.00 0.00 0.00 3.16
7241 12783 8.538409 AATTTCTGTTTCATTGCAAGATTACC 57.462 30.769 4.94 0.00 0.00 2.85
7242 12784 6.647334 TTCTGTTTCATTGCAAGATTACCA 57.353 33.333 4.94 0.00 0.00 3.25
7243 12785 6.839124 TCTGTTTCATTGCAAGATTACCAT 57.161 33.333 4.94 0.00 0.00 3.55
7283 12825 9.081997 ACTAATATTGTTGTGTTGTTGTTGTTG 57.918 29.630 0.00 0.00 0.00 3.33
7284 12826 7.897575 AATATTGTTGTGTTGTTGTTGTTGT 57.102 28.000 0.00 0.00 0.00 3.32
7285 12827 7.897575 ATATTGTTGTGTTGTTGTTGTTGTT 57.102 28.000 0.00 0.00 0.00 2.83
7286 12828 5.395325 TTGTTGTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
7287 12829 4.433615 TGTTGTGTTGTTGTTGTTGTTGT 58.566 34.783 0.00 0.00 0.00 3.32
7288 12830 4.504461 TGTTGTGTTGTTGTTGTTGTTGTC 59.496 37.500 0.00 0.00 0.00 3.18
7289 12831 4.307443 TGTGTTGTTGTTGTTGTTGTCA 57.693 36.364 0.00 0.00 0.00 3.58
8031 13627 4.719026 ATGAGATGTGCCCATTCTACAT 57.281 40.909 0.00 0.00 37.72 2.29
8155 13751 2.831333 ACTATCATTCAGGCTCTTGCG 58.169 47.619 0.00 0.00 40.82 4.85
8278 13874 0.179161 ATAGTGTCTCTGCGTCGTGC 60.179 55.000 0.00 0.00 46.70 5.34
8462 14058 9.598517 GGATTATAAGAATGATCAAGAGCCTAG 57.401 37.037 0.00 0.00 0.00 3.02
8523 14119 4.277476 ACAAACACAACTCCATTCTTCCA 58.723 39.130 0.00 0.00 0.00 3.53
8560 14156 2.615447 CCTCGACTACTACACGGCAATA 59.385 50.000 0.00 0.00 0.00 1.90
8567 14163 4.577693 ACTACTACACGGCAATATTCGAGA 59.422 41.667 3.79 0.00 0.00 4.04
8568 14164 4.585955 ACTACACGGCAATATTCGAGAT 57.414 40.909 3.79 0.00 0.00 2.75
8601 14197 1.909302 TCTCCCAAGGGATGACAAGAC 59.091 52.381 8.58 0.00 44.24 3.01
8632 14228 2.331132 GGAGCAGCACTGTCTTGCC 61.331 63.158 8.85 2.66 44.14 4.52
8795 14391 1.153086 CTGCTGGATGGCTACCACC 60.153 63.158 0.00 0.00 35.80 4.61
8851 14447 4.903045 TTACCTTGGTTGGAAGAGTAGG 57.097 45.455 0.00 0.00 0.00 3.18
9004 14609 1.499007 AGCCTGACTTCTTTCCCCAAA 59.501 47.619 0.00 0.00 0.00 3.28
9017 14622 2.722094 TCCCCAAATTCAGATGGAACG 58.278 47.619 0.00 0.00 38.60 3.95
9082 14698 4.461081 GTCTGTCTACTCACTGGTCATCTT 59.539 45.833 0.00 0.00 0.00 2.40
9097 14816 6.595682 TGGTCATCTTAATTCAGAGGAATCC 58.404 40.000 5.62 5.11 42.87 3.01
9117 14836 1.604604 GCACCAGGAGTTGCTGTAAA 58.395 50.000 0.00 0.00 0.00 2.01
9215 14940 0.180642 TGTGGTTTGCTCCCGTTGTA 59.819 50.000 0.00 0.00 0.00 2.41
9229 14954 4.098960 TCCCGTTGTACTAGGATTGACATC 59.901 45.833 0.00 0.00 0.00 3.06
9230 14955 4.099573 CCCGTTGTACTAGGATTGACATCT 59.900 45.833 0.00 0.00 0.00 2.90
9279 15022 1.457346 AAGCTATGCAGGCACAAGAC 58.543 50.000 15.25 2.31 0.00 3.01
9280 15023 0.325933 AGCTATGCAGGCACAAGACA 59.674 50.000 15.25 0.00 0.00 3.41
9301 15044 1.755179 GCCTGTTGCATGTGTCCTAT 58.245 50.000 0.00 0.00 40.77 2.57
9312 15074 9.109393 GTTGCATGTGTCCTATTTTTCTAGATA 57.891 33.333 0.00 0.00 0.00 1.98
9319 15081 9.614792 GTGTCCTATTTTTCTAGATAATGTGGT 57.385 33.333 9.66 0.00 0.00 4.16
9338 15100 2.074576 GTACTTCTTTTCTGGCGGGTC 58.925 52.381 0.00 0.00 0.00 4.46
9343 15105 0.321671 CTTTTCTGGCGGGTCAGAGA 59.678 55.000 2.95 0.00 43.64 3.10
9344 15106 0.984230 TTTTCTGGCGGGTCAGAGAT 59.016 50.000 2.95 0.00 43.64 2.75
9345 15107 0.250234 TTTCTGGCGGGTCAGAGATG 59.750 55.000 2.95 0.00 43.64 2.90
9346 15108 2.202987 CTGGCGGGTCAGAGATGC 60.203 66.667 0.00 0.00 36.93 3.91
9350 15112 2.541120 GCGGGTCAGAGATGCATGC 61.541 63.158 11.82 11.82 0.00 4.06
9354 15116 2.149578 GGGTCAGAGATGCATGCATAC 58.850 52.381 32.27 26.25 36.70 2.39
9530 15401 2.846206 AGATCCAGCTCACACCCAAATA 59.154 45.455 0.00 0.00 0.00 1.40
9545 15416 6.183360 ACACCCAAATATGTGCAATATGGAAG 60.183 38.462 0.00 0.00 35.90 3.46
9623 15499 5.948992 AAGAAGGGTCTTTCGAAGAATTG 57.051 39.130 0.00 0.00 41.55 2.32
9650 15526 1.067142 ACCGTCTGCGCTTCTCATTTA 60.067 47.619 9.73 0.00 36.67 1.40
9737 15623 7.840931 TGAGATCATCAGTGTGTTAGTATGTT 58.159 34.615 0.00 0.00 32.77 2.71
9738 15624 8.966868 TGAGATCATCAGTGTGTTAGTATGTTA 58.033 33.333 0.00 0.00 32.77 2.41
9739 15625 9.239002 GAGATCATCAGTGTGTTAGTATGTTAC 57.761 37.037 0.00 0.00 0.00 2.50
9740 15626 8.198109 AGATCATCAGTGTGTTAGTATGTTACC 58.802 37.037 0.00 0.00 0.00 2.85
9797 15685 1.654317 CTGGAAGCAGTCATCAGAGC 58.346 55.000 0.00 0.00 0.00 4.09
9812 15700 2.203538 AGCCTTGGCCAACACAGG 60.204 61.111 16.05 15.93 33.30 4.00
9815 15703 2.601367 CTTGGCCAACACAGGGGG 60.601 66.667 16.05 0.00 0.00 5.40
9816 15704 3.434179 TTGGCCAACACAGGGGGT 61.434 61.111 16.05 0.00 0.00 4.95
9817 15705 2.075355 CTTGGCCAACACAGGGGGTA 62.075 60.000 16.05 0.00 0.00 3.69
9818 15706 1.439524 TTGGCCAACACAGGGGGTAT 61.440 55.000 16.05 0.00 0.00 2.73
9819 15707 1.076995 GGCCAACACAGGGGGTATC 60.077 63.158 0.00 0.00 0.00 2.24
9821 15709 0.331616 GCCAACACAGGGGGTATCTT 59.668 55.000 0.00 0.00 0.00 2.40
9822 15710 1.682087 GCCAACACAGGGGGTATCTTC 60.682 57.143 0.00 0.00 0.00 2.87
9823 15711 1.406887 CCAACACAGGGGGTATCTTCG 60.407 57.143 0.00 0.00 0.00 3.79
9829 15717 1.383525 GGGGGTATCTTCGGGTGGA 60.384 63.158 0.00 0.00 0.00 4.02
9855 15743 0.723981 GCGAAGATGGCTGTCTGTTC 59.276 55.000 0.00 0.00 0.00 3.18
9859 15747 3.406764 GAAGATGGCTGTCTGTTCTGTT 58.593 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
489 498 5.074584 AGTGAGGATCTTCGTACCTTTTC 57.925 43.478 0.00 0.00 34.92 2.29
495 504 3.280295 TGGAGAGTGAGGATCTTCGTAC 58.720 50.000 0.00 0.00 34.92 3.67
499 508 1.412343 GCCTGGAGAGTGAGGATCTTC 59.588 57.143 0.00 0.00 34.92 2.87
539 548 0.907230 GGGAGAGCTAGCTATGGGGG 60.907 65.000 18.30 0.00 0.00 5.40
632 641 0.815213 TGTTGTCACCTGCAGAGTGC 60.815 55.000 22.98 18.98 45.29 4.40
633 642 1.888215 ATGTTGTCACCTGCAGAGTG 58.112 50.000 17.39 20.48 36.54 3.51
634 643 2.645838 AATGTTGTCACCTGCAGAGT 57.354 45.000 17.39 8.77 0.00 3.24
635 644 3.635331 CAAAATGTTGTCACCTGCAGAG 58.365 45.455 17.39 8.04 0.00 3.35
636 645 2.223782 GCAAAATGTTGTCACCTGCAGA 60.224 45.455 17.39 0.00 37.06 4.26
643 652 4.032703 ACACAGAGCAAAATGTTGTCAC 57.967 40.909 0.00 0.00 37.06 3.67
755 766 7.247019 GGAGCAAAATGAGTGAATCTAAACTC 58.753 38.462 0.00 0.00 42.61 3.01
759 770 5.245531 ACGGAGCAAAATGAGTGAATCTAA 58.754 37.500 0.00 0.00 0.00 2.10
807 818 8.039538 CCCTCCGTTCCTAAATATAAGGTATTC 58.960 40.741 4.41 0.00 35.48 1.75
811 822 5.470501 TCCCTCCGTTCCTAAATATAAGGT 58.529 41.667 4.41 0.00 35.48 3.50
889 1044 2.687935 TCGAGCCTTCCCAAAAATATGC 59.312 45.455 0.00 0.00 0.00 3.14
949 1104 2.116983 GACTCCTCAGCAGTTGGGCA 62.117 60.000 0.00 0.00 35.83 5.36
1177 1418 3.439293 CACTCATGCGACACCTACTAAG 58.561 50.000 0.00 0.00 0.00 2.18
1243 2983 5.399113 TGGTTAAATCTGGCCTAAAGGTTT 58.601 37.500 3.32 4.53 37.57 3.27
3054 5163 5.387788 TGTCTTTAGGATATTGCCATGCAT 58.612 37.500 0.00 0.00 38.76 3.96
3055 5164 4.790937 TGTCTTTAGGATATTGCCATGCA 58.209 39.130 0.00 0.00 36.47 3.96
3072 5181 2.620115 CCTTGTTGTGCAGTCATGTCTT 59.380 45.455 0.00 0.00 0.00 3.01
3669 6302 6.994496 TGCCAAGACTTCATATTTCCAGATAG 59.006 38.462 0.00 0.00 0.00 2.08
3896 6765 4.574828 ACGGTAAGCTGCAAATCGATTTAT 59.425 37.500 22.33 0.00 0.00 1.40
3962 6831 5.286438 TGGAATCTGTTCATTACGATACCG 58.714 41.667 0.00 0.00 37.69 4.02
3988 6858 6.549433 AATGTTGGATGTCTTATGCCAATT 57.451 33.333 0.00 0.00 41.89 2.32
4167 7046 6.648879 TTTACCTTTTGGAGACCAGATTTG 57.351 37.500 0.00 0.00 44.07 2.32
4217 7097 7.394641 ACACTGAAGACTGTAGAGACATCATTA 59.605 37.037 0.00 0.00 34.24 1.90
4226 7106 7.721286 ATTTGAAACACTGAAGACTGTAGAG 57.279 36.000 0.00 0.00 0.00 2.43
4267 7147 8.284945 GGTAAAACCCGGAATTTACTCTAATT 57.715 34.615 26.91 7.21 40.30 1.40
4285 7165 8.779303 CAAAAATGTCAAAATAGGGGGTAAAAC 58.221 33.333 0.00 0.00 0.00 2.43
4325 7205 6.824305 AAACAGATGAACTCCCACTAAATG 57.176 37.500 0.00 0.00 0.00 2.32
4337 7217 6.071616 TGCTAAATGGGGTAAAACAGATGAAC 60.072 38.462 0.00 0.00 0.00 3.18
4371 7251 7.957992 AATATTAAACGGGGTAAATTGTGGA 57.042 32.000 0.00 0.00 0.00 4.02
4453 7380 6.349115 CCATGATCTGTTGCAAATATAGGAGC 60.349 42.308 0.00 0.00 0.00 4.70
4457 7385 6.889301 ACCCATGATCTGTTGCAAATATAG 57.111 37.500 0.00 0.00 0.00 1.31
4458 7386 9.448438 GTATACCCATGATCTGTTGCAAATATA 57.552 33.333 0.00 0.00 0.00 0.86
4459 7387 7.944000 TGTATACCCATGATCTGTTGCAAATAT 59.056 33.333 0.00 0.00 0.00 1.28
4632 7561 7.011857 GGAGGACAAGATGATGTTAATCAGTTC 59.988 40.741 0.00 0.00 45.88 3.01
4698 7627 0.107703 TTGTAAGGCGCAGAGATGGG 60.108 55.000 10.83 0.00 0.00 4.00
5003 8161 0.821711 TGAACAAACAAGCCCCCTCG 60.822 55.000 0.00 0.00 0.00 4.63
5102 8421 0.324943 TCTTCTTCCTCCTTTGGCGG 59.675 55.000 0.00 0.00 0.00 6.13
5484 8822 2.742372 GGTGGTCGCTTGCGTCAT 60.742 61.111 14.70 0.00 0.00 3.06
5491 8829 4.778143 GCCCGATGGTGGTCGCTT 62.778 66.667 0.00 0.00 40.17 4.68
5585 8931 2.514803 ACTGTTAGGTCCAATTGGCAC 58.485 47.619 20.33 17.12 34.44 5.01
5592 8938 2.414612 AGTCCCAACTGTTAGGTCCAA 58.585 47.619 4.93 0.00 33.32 3.53
5787 9134 2.925563 GCATTATGCAGTCCAAACAAGC 59.074 45.455 12.80 0.00 44.26 4.01
5876 9661 2.754552 TCATGCCAGTAAGTCATTTGCC 59.245 45.455 0.00 0.00 0.00 4.52
5905 9691 3.250744 CATGTGTTACCGTGGTACTCAG 58.749 50.000 0.00 0.00 0.00 3.35
5906 9692 2.610976 GCATGTGTTACCGTGGTACTCA 60.611 50.000 0.00 0.00 0.00 3.41
6210 10007 2.092211 CGTTGTGACGCTGAAGTATTCC 59.908 50.000 0.00 0.00 43.15 3.01
6480 11922 1.607148 GTGCTTGAAGGGGTGTAACAC 59.393 52.381 0.00 0.00 41.97 3.32
6521 12055 2.033550 CACTAGGGTTGTAGCTAGCTCG 59.966 54.545 23.26 2.32 0.00 5.03
6543 12077 8.054152 TGTCTTTTTACGGTTTTCTTTAGGTT 57.946 30.769 0.00 0.00 0.00 3.50
6703 12243 6.980593 ACAAGAACATGCTTGCTTGTATTTA 58.019 32.000 17.95 0.00 46.37 1.40
6927 12469 5.887598 GCCATGTCATTAGGATATTGCCATA 59.112 40.000 0.00 0.00 31.95 2.74
7096 12638 3.733960 GGTTTGAAGGACCGGCGC 61.734 66.667 0.00 0.00 0.00 6.53
7271 12813 5.403766 TGACAATGACAACAACAACAACAAC 59.596 36.000 0.00 0.00 0.00 3.32
7272 12814 5.532557 TGACAATGACAACAACAACAACAA 58.467 33.333 0.00 0.00 0.00 2.83
7274 12816 6.645700 AATGACAATGACAACAACAACAAC 57.354 33.333 0.00 0.00 0.00 3.32
7275 12817 8.939201 AATAATGACAATGACAACAACAACAA 57.061 26.923 0.00 0.00 0.00 2.83
7391 12958 3.532641 ATTTCCCTGGGGCAGATAATC 57.467 47.619 14.00 0.00 32.44 1.75
7491 13070 4.771577 TGGAATTGTTGATTGTGCCATAGT 59.228 37.500 0.00 0.00 0.00 2.12
8031 13627 2.937519 TGGCTGACATGTAACCAAACA 58.062 42.857 10.66 0.00 0.00 2.83
8278 13874 0.817634 TGAACTCAAAGGGCACACCG 60.818 55.000 0.00 0.00 46.96 4.94
8523 14119 3.447944 GTCGAGGGTCTCCAAGTATCTTT 59.552 47.826 0.00 0.00 34.83 2.52
8560 14156 7.319646 GGAGAGCAACATCTATTATCTCGAAT 58.680 38.462 0.00 0.00 34.01 3.34
8567 14163 5.222007 CCCTTGGGAGAGCAACATCTATTAT 60.222 44.000 0.00 0.00 0.00 1.28
8568 14164 4.103153 CCCTTGGGAGAGCAACATCTATTA 59.897 45.833 0.00 0.00 0.00 0.98
8601 14197 1.148157 CTGCTCCGTGCTAATCCGTG 61.148 60.000 0.00 0.00 43.37 4.94
8632 14228 5.062683 CGCGATTAAACTGATGATATCCCTG 59.937 44.000 0.00 0.00 0.00 4.45
8851 14447 1.461127 GCAGAAGACACGACCAACATC 59.539 52.381 0.00 0.00 0.00 3.06
8938 14539 8.788806 ACGGAACACAAATCACTGAATTATTAA 58.211 29.630 0.00 0.00 0.00 1.40
8940 14541 7.214467 ACGGAACACAAATCACTGAATTATT 57.786 32.000 0.00 0.00 0.00 1.40
8941 14542 6.817765 ACGGAACACAAATCACTGAATTAT 57.182 33.333 0.00 0.00 0.00 1.28
8942 14543 6.261158 TCAACGGAACACAAATCACTGAATTA 59.739 34.615 0.00 0.00 0.00 1.40
8943 14544 5.067153 TCAACGGAACACAAATCACTGAATT 59.933 36.000 0.00 0.00 0.00 2.17
8944 14545 4.578516 TCAACGGAACACAAATCACTGAAT 59.421 37.500 0.00 0.00 0.00 2.57
8961 14562 7.225538 GGCTATAGAAATATCATGGATCAACGG 59.774 40.741 3.21 0.00 0.00 4.44
9004 14609 2.479566 AGCACACGTTCCATCTGAAT 57.520 45.000 0.00 0.00 34.90 2.57
9017 14622 5.748630 GCAAAGCCCTTAATTATAAGCACAC 59.251 40.000 0.00 0.00 37.74 3.82
9082 14698 2.503765 TGGTGCGGATTCCTCTGAATTA 59.496 45.455 0.30 0.00 41.30 1.40
9117 14836 1.632046 CGTTGGCTGTCGCGGTATTT 61.632 55.000 6.13 0.00 36.88 1.40
9215 14940 7.456269 CCCCTAATTAGAGATGTCAATCCTAGT 59.544 40.741 14.28 0.00 32.77 2.57
9229 14954 9.094578 TCATCTCTAAACATCCCCTAATTAGAG 57.905 37.037 14.28 12.42 45.51 2.43
9230 14955 9.621239 ATCATCTCTAAACATCCCCTAATTAGA 57.379 33.333 14.28 0.00 33.08 2.10
9239 14982 8.457238 AGCTTTTAATCATCTCTAAACATCCC 57.543 34.615 0.00 0.00 0.00 3.85
9312 15074 3.502211 CGCCAGAAAAGAAGTACCACATT 59.498 43.478 0.00 0.00 0.00 2.71
9319 15081 1.695242 TGACCCGCCAGAAAAGAAGTA 59.305 47.619 0.00 0.00 0.00 2.24
9354 15116 7.541091 GCATATTGCATAAATCTGGAAGACATG 59.459 37.037 0.00 0.00 45.54 3.21
9383 15145 5.106157 GCAGCAGAAGAGGTTTAAAGCATTA 60.106 40.000 18.91 0.00 0.00 1.90
9384 15146 4.321527 GCAGCAGAAGAGGTTTAAAGCATT 60.322 41.667 18.91 12.74 0.00 3.56
9385 15147 3.192212 GCAGCAGAAGAGGTTTAAAGCAT 59.808 43.478 18.91 4.88 0.00 3.79
9386 15148 2.554032 GCAGCAGAAGAGGTTTAAAGCA 59.446 45.455 18.91 0.00 0.00 3.91
9387 15149 2.816672 AGCAGCAGAAGAGGTTTAAAGC 59.183 45.455 9.39 9.39 0.00 3.51
9523 15394 5.786311 CCTTCCATATTGCACATATTTGGG 58.214 41.667 6.53 3.43 0.00 4.12
9530 15401 3.484407 GAGAGCCTTCCATATTGCACAT 58.516 45.455 0.00 0.00 0.00 3.21
9623 15499 4.683334 GCGCAGACGGTTGTTGGC 62.683 66.667 0.30 0.00 40.57 4.52
9650 15526 7.759489 AATTAAACTGTGTCACACATACCAT 57.241 32.000 12.04 0.00 43.71 3.55
9735 15621 2.744202 CTCCTGTTGCTGTCATGGTAAC 59.256 50.000 0.00 0.00 0.00 2.50
9737 15623 1.339055 GCTCCTGTTGCTGTCATGGTA 60.339 52.381 0.00 0.00 0.00 3.25
9738 15624 0.607489 GCTCCTGTTGCTGTCATGGT 60.607 55.000 0.00 0.00 0.00 3.55
9739 15625 0.322277 AGCTCCTGTTGCTGTCATGG 60.322 55.000 0.00 0.00 39.56 3.66
9740 15626 3.244764 AGCTCCTGTTGCTGTCATG 57.755 52.632 0.00 0.00 39.56 3.07
9797 15685 2.601367 CCCCTGTGTTGGCCAAGG 60.601 66.667 21.21 16.80 0.00 3.61
9812 15700 0.979187 TGTCCACCCGAAGATACCCC 60.979 60.000 0.00 0.00 0.00 4.95
9815 15703 3.754766 GGTGTCCACCCGAAGATAC 57.245 57.895 5.08 0.00 45.68 2.24
9829 15717 2.045926 GCCATCTTCGCCTGGTGT 60.046 61.111 7.20 0.00 34.86 4.16
9855 15743 3.299585 CGATACGAGCGCCAACAG 58.700 61.111 2.29 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.