Multiple sequence alignment - TraesCS6D01G404900

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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 TraesCS6D01G404900 chr6D 100.000 8612 0 0 1 8612 472431085 472422474 0.000000e+00 15904.0
1 TraesCS6D01G404900 chr6D 82.861 776 75 21 2401 3151 472500932 472500190 2.030000e-180 643.0
2 TraesCS6D01G404900 chr6D 84.832 567 47 11 5319 5854 472498059 472497501 1.270000e-147 534.0
3 TraesCS6D01G404900 chr6D 79.564 734 86 28 745 1441 472502549 472501843 4.710000e-127 466.0
4 TraesCS6D01G404900 chr6D 83.368 487 54 9 3152 3615 472499955 472499473 7.990000e-115 425.0
5 TraesCS6D01G404900 chr6D 90.596 319 28 2 6224 6540 472958228 472957910 1.030000e-113 422.0
6 TraesCS6D01G404900 chr6D 77.897 561 89 19 5485 6040 472489198 472488668 5.020000e-82 316.0
7 TraesCS6D01G404900 chr6D 87.143 280 30 5 7062 7336 339272360 339272638 6.490000e-81 313.0
8 TraesCS6D01G404900 chr6D 85.764 288 39 2 278 565 472504649 472504364 3.910000e-78 303.0
9 TraesCS6D01G404900 chr6D 90.957 188 14 1 7337 7524 472497264 472497080 5.160000e-62 250.0
10 TraesCS6D01G404900 chr6D 80.333 300 47 8 6680 6970 124947678 124947382 5.240000e-52 217.0
11 TraesCS6D01G404900 chr6D 79.580 333 42 13 7572 7890 472497086 472496766 1.880000e-51 215.0
12 TraesCS6D01G404900 chr6D 88.966 145 16 0 6538 6682 180342631 180342775 6.870000e-41 180.0
13 TraesCS6D01G404900 chr6D 79.913 229 31 6 8276 8504 472496228 472496015 4.160000e-33 154.0
14 TraesCS6D01G404900 chr6D 95.556 90 4 0 4638 4727 472498412 472498323 2.510000e-30 145.0
15 TraesCS6D01G404900 chr6D 87.156 109 13 1 6114 6222 436407794 436407901 1.170000e-23 122.0
16 TraesCS6D01G404900 chr6D 81.379 145 16 7 3621 3765 472499492 472499359 3.290000e-19 108.0
17 TraesCS6D01G404900 chr6D 100.000 28 0 0 326 353 445738296 445738269 1.600000e-02 52.8
18 TraesCS6D01G404900 chr1A 95.806 5150 135 22 973 6048 2843882 2838740 0.000000e+00 8239.0
19 TraesCS6D01G404900 chr1A 93.516 1789 79 10 6092 7852 2838741 2836962 0.000000e+00 2627.0
20 TraesCS6D01G404900 chr1A 84.848 1353 144 18 3165 4490 2657577 2656259 0.000000e+00 1306.0
21 TraesCS6D01G404900 chr1A 90.996 522 22 2 8116 8612 2836363 2835842 0.000000e+00 680.0
22 TraesCS6D01G404900 chr1A 78.586 976 109 51 552 1441 2648329 2647368 3.510000e-153 553.0
23 TraesCS6D01G404900 chr1A 84.303 567 50 13 5319 5854 2643803 2643245 1.280000e-142 518.0
24 TraesCS6D01G404900 chr1A 81.803 588 74 11 7334 7894 2653588 2653007 6.090000e-126 462.0
25 TraesCS6D01G404900 chr1A 86.095 338 36 6 4985 5317 2655781 2655450 3.820000e-93 353.0
26 TraesCS6D01G404900 chr1A 96.226 212 6 2 4815 5025 2826143 2825933 6.400000e-91 346.0
27 TraesCS6D01G404900 chr1A 86.392 316 40 3 5735 6047 2653965 2653650 8.280000e-90 342.0
28 TraesCS6D01G404900 chr1A 83.377 379 34 11 2775 3143 2646189 2645830 3.000000e-84 324.0
29 TraesCS6D01G404900 chr1A 84.871 271 26 5 2389 2645 2646468 2646199 8.580000e-65 259.0
30 TraesCS6D01G404900 chr1A 90.426 188 15 1 7337 7524 2643006 2642822 2.400000e-60 244.0
31 TraesCS6D01G404900 chr1A 93.056 144 10 0 4626 4769 2655988 2655845 2.440000e-50 211.0
32 TraesCS6D01G404900 chr1A 78.979 333 44 12 7572 7890 2642828 2642508 4.080000e-48 204.0
33 TraesCS6D01G404900 chr1A 86.628 172 20 2 3454 3622 2645382 2645211 4.100000e-43 187.0
34 TraesCS6D01G404900 chr1A 90.909 132 12 0 6551 6682 248034405 248034274 2.470000e-40 178.0
35 TraesCS6D01G404900 chr1A 95.506 89 4 0 5082 5170 2825930 2825842 9.010000e-30 143.0
36 TraesCS6D01G404900 chr1A 93.333 90 6 0 4638 4727 2644155 2644066 5.420000e-27 134.0
37 TraesCS6D01G404900 chr1A 82.069 145 15 7 3621 3765 2645238 2645105 7.070000e-21 113.0
38 TraesCS6D01G404900 chr1A 90.769 65 6 0 6968 7032 163834555 163834619 4.280000e-13 87.9
39 TraesCS6D01G404900 chr1A 90.769 65 6 0 6968 7032 163956808 163956872 4.280000e-13 87.9
40 TraesCS6D01G404900 chr1A 87.671 73 9 0 7891 7963 2695247 2695175 1.540000e-12 86.1
41 TraesCS6D01G404900 chr1A 100.000 34 0 0 7866 7899 2836966 2836933 7.220000e-06 63.9
42 TraesCS6D01G404900 chr6A 95.760 3255 91 11 200 3411 617551598 617554848 0.000000e+00 5203.0
43 TraesCS6D01G404900 chr6A 95.988 2642 60 14 3450 6048 617555170 617557808 0.000000e+00 4250.0
44 TraesCS6D01G404900 chr6A 93.040 1839 81 19 6092 7899 617557807 617559629 0.000000e+00 2643.0
45 TraesCS6D01G404900 chr6A 87.259 777 79 10 3725 4490 617237648 617238415 0.000000e+00 869.0
46 TraesCS6D01G404900 chr6A 84.785 769 96 6 3730 4490 617224235 617224990 0.000000e+00 752.0
47 TraesCS6D01G404900 chr6A 90.684 526 20 5 8116 8612 617560142 617560667 0.000000e+00 673.0
48 TraesCS6D01G404900 chr6A 86.312 621 69 10 5440 6045 617351752 617352371 0.000000e+00 662.0
49 TraesCS6D01G404900 chr6A 84.264 591 54 7 2389 2966 617349429 617349993 2.740000e-149 540.0
50 TraesCS6D01G404900 chr6A 83.717 565 54 15 5319 5854 617322413 617322968 4.640000e-137 499.0
51 TraesCS6D01G404900 chr6A 85.232 474 60 2 3250 3723 617237217 617237680 6.050000e-131 479.0
52 TraesCS6D01G404900 chr6A 86.861 411 51 2 245 655 617234082 617234489 2.830000e-124 457.0
53 TraesCS6D01G404900 chr6A 79.340 697 95 28 745 1406 617317983 617318665 2.210000e-120 444.0
54 TraesCS6D01G404900 chr6A 86.600 403 53 1 4089 4490 617350450 617350852 2.210000e-120 444.0
55 TraesCS6D01G404900 chr6A 83.468 496 53 16 7334 7802 617352435 617352928 1.330000e-117 435.0
56 TraesCS6D01G404900 chr6A 85.383 431 42 14 2726 3143 617319875 617320297 2.220000e-115 427.0
57 TraesCS6D01G404900 chr6A 79.154 662 70 36 712 1318 617217210 617217858 6.270000e-106 396.0
58 TraesCS6D01G404900 chr6A 80.612 490 79 11 2674 3149 617236346 617236833 1.770000e-96 364.0
59 TraesCS6D01G404900 chr6A 98.507 201 3 0 1 201 617551358 617551558 1.060000e-93 355.0
60 TraesCS6D01G404900 chr6A 92.653 245 18 0 5486 5730 617239443 617239687 3.820000e-93 353.0
61 TraesCS6D01G404900 chr6A 91.600 250 7 6 654 889 617317728 617317977 4.980000e-87 333.0
62 TraesCS6D01G404900 chr6A 84.337 332 52 0 200 531 617232598 617232929 8.340000e-85 326.0
63 TraesCS6D01G404900 chr6A 86.411 287 25 5 2389 2662 617319567 617319852 1.400000e-77 302.0
64 TraesCS6D01G404900 chr6A 83.596 317 32 10 1121 1425 617234884 617235192 6.580000e-71 279.0
65 TraesCS6D01G404900 chr6A 90.909 209 18 1 4984 5192 617351327 617351534 6.580000e-71 279.0
66 TraesCS6D01G404900 chr6A 89.401 217 16 4 5828 6041 617239747 617239959 5.130000e-67 267.0
67 TraesCS6D01G404900 chr6A 80.243 329 44 15 998 1316 617246646 617246963 2.420000e-55 228.0
68 TraesCS6D01G404900 chr6A 85.845 219 22 5 5101 5317 617239011 617239222 3.130000e-54 224.0
69 TraesCS6D01G404900 chr6A 87.845 181 15 3 2407 2580 617236127 617236307 1.130000e-48 206.0
70 TraesCS6D01G404900 chr6A 85.572 201 17 7 3 201 617233784 617233974 5.270000e-47 200.0
71 TraesCS6D01G404900 chr6A 80.357 280 29 12 1143 1416 617348294 617348553 1.140000e-43 189.0
72 TraesCS6D01G404900 chr6A 83.673 147 23 1 247 393 617253227 617253372 4.190000e-28 137.0
73 TraesCS6D01G404900 chr6A 91.892 74 6 0 4984 5057 617238935 617239008 4.250000e-18 104.0
74 TraesCS6D01G404900 chr6A 83.962 106 15 2 1632 1736 617218153 617218257 5.500000e-17 100.0
75 TraesCS6D01G404900 chr6B 93.917 3436 86 35 2316 5676 717141701 717138314 0.000000e+00 5073.0
76 TraesCS6D01G404900 chr6B 94.695 1263 44 10 187 1435 717143944 717142691 0.000000e+00 1940.0
77 TraesCS6D01G404900 chr6B 95.159 785 31 5 7121 7899 717137891 717137108 0.000000e+00 1232.0
78 TraesCS6D01G404900 chr6B 87.751 996 96 9 3502 4490 717401647 717400671 0.000000e+00 1140.0
79 TraesCS6D01G404900 chr6B 91.701 723 56 3 7891 8611 717115981 717115261 0.000000e+00 1000.0
80 TraesCS6D01G404900 chr6B 94.836 639 28 4 1693 2331 717142379 717141746 0.000000e+00 992.0
81 TraesCS6D01G404900 chr6B 80.797 953 141 31 1750 2678 717403433 717402499 0.000000e+00 708.0
82 TraesCS6D01G404900 chr6B 86.078 668 68 8 3831 4492 717417789 717417141 0.000000e+00 695.0
83 TraesCS6D01G404900 chr6B 85.714 616 68 11 5440 6047 717399634 717399031 4.390000e-177 632.0
84 TraesCS6D01G404900 chr6B 79.896 766 104 30 712 1441 717420719 717419968 4.610000e-142 516.0
85 TraesCS6D01G404900 chr6B 88.942 416 30 5 6668 7068 717138317 717137903 4.640000e-137 499.0
86 TraesCS6D01G404900 chr6B 87.119 427 41 6 2726 3143 717418764 717418343 1.010000e-128 472.0
87 TraesCS6D01G404900 chr6B 85.622 466 46 12 5319 5772 717416249 717415793 3.640000e-128 470.0
88 TraesCS6D01G404900 chr6B 86.647 337 35 6 4985 5317 717400180 717399850 1.770000e-96 364.0
89 TraesCS6D01G404900 chr6B 97.487 199 5 0 3 201 717144170 717143972 2.980000e-89 340.0
90 TraesCS6D01G404900 chr6B 87.097 279 22 5 2389 2654 717419070 717418793 3.910000e-78 303.0
91 TraesCS6D01G404900 chr6B 93.960 149 9 0 4621 4769 717416836 717416688 8.700000e-55 226.0
92 TraesCS6D01G404900 chr6B 81.979 283 30 13 1146 1423 717403955 717403689 4.050000e-53 220.0
93 TraesCS6D01G404900 chr6B 88.757 169 15 4 4794 4960 704099409 704099243 4.080000e-48 204.0
94 TraesCS6D01G404900 chr6B 90.728 151 12 1 4621 4769 717400394 717400244 5.270000e-47 200.0
95 TraesCS6D01G404900 chr6B 81.356 236 42 2 5807 6040 717408005 717407770 3.170000e-44 191.0
96 TraesCS6D01G404900 chr6B 80.816 245 38 7 2123 2364 717411183 717410945 5.310000e-42 183.0
97 TraesCS6D01G404900 chr6B 90.909 132 12 0 4492 4623 717417079 717416948 2.470000e-40 178.0
98 TraesCS6D01G404900 chr6B 90.769 130 12 0 7334 7463 717398969 717398840 3.200000e-39 174.0
99 TraesCS6D01G404900 chr6B 91.667 120 4 1 1433 1546 717142588 717142469 2.490000e-35 161.0
100 TraesCS6D01G404900 chr6B 86.207 145 19 1 3621 3765 717417963 717417820 1.160000e-33 156.0
101 TraesCS6D01G404900 chr6B 75.375 333 68 6 8271 8603 717414328 717414010 1.940000e-31 148.0
102 TraesCS6D01G404900 chr6B 88.785 107 12 0 6116 6222 448670912 448670806 1.950000e-26 132.0
103 TraesCS6D01G404900 chr6B 92.593 54 4 0 3527 3580 717418028 717417975 2.580000e-10 78.7
104 TraesCS6D01G404900 chr5D 94.771 306 15 1 7962 8267 221824578 221824274 7.820000e-130 475.0
105 TraesCS6D01G404900 chr5D 89.967 299 19 3 7051 7338 210677899 210678197 8.160000e-100 375.0
106 TraesCS6D01G404900 chr5D 82.609 299 39 8 6681 6969 210677899 210678194 1.440000e-62 252.0
107 TraesCS6D01G404900 chr5D 79.817 327 46 12 6680 6990 354809097 354808775 4.050000e-53 220.0
108 TraesCS6D01G404900 chr4B 90.252 318 27 4 6224 6538 171806343 171806027 6.220000e-111 412.0
109 TraesCS6D01G404900 chr3D 90.031 321 28 4 6227 6543 79503272 79502952 6.220000e-111 412.0
110 TraesCS6D01G404900 chr3D 90.291 309 30 0 7959 8267 420987233 420987541 1.040000e-108 405.0
111 TraesCS6D01G404900 chr3D 88.449 303 24 4 7051 7342 175803379 175803077 1.060000e-93 355.0
112 TraesCS6D01G404900 chr3D 86.598 291 33 4 7051 7336 524486669 524486380 5.020000e-82 316.0
113 TraesCS6D01G404900 chr3D 90.173 173 6 5 4794 4956 580128344 580128515 1.880000e-51 215.0
114 TraesCS6D01G404900 chr3A 90.820 305 28 0 7963 8267 644530532 644530228 8.050000e-110 409.0
115 TraesCS6D01G404900 chr3A 89.655 145 15 0 6538 6682 698757007 698757151 1.480000e-42 185.0
116 TraesCS6D01G404900 chr3A 84.492 187 28 1 16 201 492732646 492732832 5.310000e-42 183.0
117 TraesCS6D01G404900 chr3A 91.089 101 9 0 6122 6222 28327028 28326928 4.190000e-28 137.0
118 TraesCS6D01G404900 chrUn 90.554 307 29 0 7961 8267 103496586 103496892 2.890000e-109 407.0
119 TraesCS6D01G404900 chr5B 90.228 307 29 1 7961 8267 11532671 11532976 4.840000e-107 399.0
120 TraesCS6D01G404900 chr5B 89.231 65 5 2 6968 7031 12039997 12040060 7.170000e-11 80.5
121 TraesCS6D01G404900 chr4D 90.228 307 24 6 7962 8267 497512349 497512650 6.270000e-106 396.0
122 TraesCS6D01G404900 chr4D 80.972 247 31 10 6681 6917 70787949 70788189 1.910000e-41 182.0
123 TraesCS6D01G404900 chr4D 79.151 259 28 14 6679 6919 108480713 108480963 1.160000e-33 156.0
124 TraesCS6D01G404900 chr4D 85.075 134 17 1 7051 7181 128404671 128404804 5.420000e-27 134.0
125 TraesCS6D01G404900 chr1B 87.736 318 22 7 6224 6538 329966624 329966927 1.060000e-93 355.0
126 TraesCS6D01G404900 chr1B 81.356 295 38 12 6681 6963 609415322 609415611 3.130000e-54 224.0
127 TraesCS6D01G404900 chr4A 86.458 288 35 3 7051 7337 661019093 661019377 6.490000e-81 313.0
128 TraesCS6D01G404900 chr4A 92.424 132 10 0 6551 6682 740756896 740756765 1.140000e-43 189.0
129 TraesCS6D01G404900 chr4A 93.103 58 4 0 6968 7025 106574557 106574500 1.540000e-12 86.1
130 TraesCS6D01G404900 chr4A 90.000 60 6 0 6969 7028 743632977 743632918 2.580000e-10 78.7
131 TraesCS6D01G404900 chr7B 83.904 292 39 8 7051 7337 688739185 688738897 1.100000e-68 272.0
132 TraesCS6D01G404900 chr7B 83.895 267 29 5 7051 7306 453770709 453770446 8.640000e-60 243.0
133 TraesCS6D01G404900 chr7B 81.169 308 31 11 6680 6969 728985749 728986047 1.130000e-53 222.0
134 TraesCS6D01G404900 chr7B 88.276 145 16 1 12 156 613472001 613472144 1.150000e-38 172.0
135 TraesCS6D01G404900 chr2D 81.789 313 38 8 6675 6969 154184981 154185292 2.400000e-60 244.0
136 TraesCS6D01G404900 chr2D 80.000 300 47 8 6681 6970 282366111 282366407 8.760000e-50 209.0
137 TraesCS6D01G404900 chr2D 92.414 145 11 0 6538 6682 375814383 375814527 3.150000e-49 207.0
138 TraesCS6D01G404900 chr2D 83.735 166 23 4 14 177 471633157 471633320 4.160000e-33 154.0
139 TraesCS6D01G404900 chr1D 80.667 300 44 7 6681 6970 111864727 111865022 4.050000e-53 220.0
140 TraesCS6D01G404900 chr1D 89.630 135 13 1 6 139 317116577 317116443 4.130000e-38 171.0
141 TraesCS6D01G404900 chr1D 89.630 135 13 1 6 139 317121903 317121769 4.130000e-38 171.0
142 TraesCS6D01G404900 chr1D 86.429 140 17 2 7334 7472 449121842 449121704 1.500000e-32 152.0
143 TraesCS6D01G404900 chr1D 88.596 114 13 0 6109 6222 486311130 486311017 1.170000e-28 139.0
144 TraesCS6D01G404900 chr1D 88.889 63 7 0 6968 7030 378750193 378750255 2.580000e-10 78.7
145 TraesCS6D01G404900 chr7D 80.471 297 30 13 6679 6958 465688897 465688612 1.470000e-47 202.0
146 TraesCS6D01G404900 chr7D 87.356 174 11 8 4794 4957 5318784 5318956 1.140000e-43 189.0
147 TraesCS6D01G404900 chr7D 87.879 165 14 5 4794 4956 571809482 571809642 1.140000e-43 189.0
148 TraesCS6D01G404900 chr7D 79.167 144 20 4 4794 4927 397201618 397201761 3.310000e-14 91.6
149 TraesCS6D01G404900 chr3B 80.142 282 43 8 6704 6975 273904037 273903759 1.900000e-46 198.0
150 TraesCS6D01G404900 chr5A 87.952 166 17 3 4794 4957 573814832 573814668 8.820000e-45 193.0
151 TraesCS6D01G404900 chr5A 89.109 101 10 1 6123 6222 353596603 353596703 3.260000e-24 124.0
152 TraesCS6D01G404900 chr2B 90.345 145 14 0 6538 6682 50023777 50023921 3.170000e-44 191.0
153 TraesCS6D01G404900 chr2B 94.595 37 1 1 4794 4829 743735706 743735742 1.000000e-03 56.5
154 TraesCS6D01G404900 chr7A 89.655 145 15 0 6538 6682 208520775 208520631 1.480000e-42 185.0
155 TraesCS6D01G404900 chr2A 84.181 177 18 4 14 190 711665875 711666041 6.920000e-36 163.0
156 TraesCS6D01G404900 chr2A 87.850 107 13 0 6116 6222 565266600 565266706 9.080000e-25 126.0
157 TraesCS6D01G404900 chr2A 85.714 112 16 0 6110 6221 540047669 540047780 1.520000e-22 119.0


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 TraesCS6D01G404900 chr6D 472422474 472431085 8611 True 15904.000000 15904 100.000000 1 8612 1 chr6D.!!$R3 8611
1 TraesCS6D01G404900 chr6D 472496015 472504649 8634 True 324.300000 643 84.377400 278 8504 10 chr6D.!!$R6 8226
2 TraesCS6D01G404900 chr6D 472488668 472489198 530 True 316.000000 316 77.897000 5485 6040 1 chr6D.!!$R4 555
3 TraesCS6D01G404900 chr1A 2835842 2843882 8040 True 2902.475000 8239 95.079500 973 8612 4 chr1A.!!$R6 7639
4 TraesCS6D01G404900 chr1A 2653007 2657577 4570 True 534.800000 1306 86.438800 3165 7894 5 chr1A.!!$R4 4729
5 TraesCS6D01G404900 chr1A 2642508 2648329 5821 True 281.777778 553 84.730222 552 7890 9 chr1A.!!$R3 7338
6 TraesCS6D01G404900 chr6A 617551358 617560667 9309 False 2624.800000 5203 94.795800 1 8612 5 chr6A.!!$F8 8611
7 TraesCS6D01G404900 chr6A 617224235 617224990 755 False 752.000000 752 84.785000 3730 4490 1 chr6A.!!$F1 760
8 TraesCS6D01G404900 chr6A 617348294 617352928 4634 False 424.833333 662 85.318333 1143 7802 6 chr6A.!!$F7 6659
9 TraesCS6D01G404900 chr6A 617317728 617322968 5240 False 401.000000 499 85.290200 654 5854 5 chr6A.!!$F6 5200
10 TraesCS6D01G404900 chr6A 617232598 617239959 7361 False 344.000000 869 86.758750 3 6041 12 chr6A.!!$F5 6038
11 TraesCS6D01G404900 chr6A 617217210 617218257 1047 False 248.000000 396 81.558000 712 1736 2 chr6A.!!$F4 1024
12 TraesCS6D01G404900 chr6B 717137108 717144170 7062 True 1462.428571 5073 93.814714 3 7899 7 chr6B.!!$R4 7896
13 TraesCS6D01G404900 chr6B 717115261 717115981 720 True 1000.000000 1000 91.701000 7891 8611 1 chr6B.!!$R3 720
14 TraesCS6D01G404900 chr6B 717398840 717420719 21879 True 371.300000 1140 85.863842 712 8603 19 chr6B.!!$R5 7891

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
431 1685 0.318762 GGATGGGACGTCTATCAGCC 59.681 60.000 24.36 21.92 0.00 4.85 F
1133 4425 0.317603 CTCACCGACGACTTCAACGT 60.318 55.000 0.00 0.00 46.58 3.99 F
2041 5723 0.531974 ATCAACACTTGTCGCCGTGT 60.532 50.000 0.00 0.00 45.55 4.49 F
2799 6651 1.461127 GTGTTTGCTACTTCAGGCTCG 59.539 52.381 0.00 0.00 0.00 5.03 F
4365 9244 1.332178 GTGAGACTGCGTTCTCTTCG 58.668 55.000 13.83 0.00 42.36 3.79 F
5655 11391 2.353208 CCTTCTGTCTACACTGTGGAGC 60.353 54.545 15.35 10.75 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 5319 1.199097 CCACGTGTGCTGTAATTTCCC 59.801 52.381 15.65 0.00 0.00 3.97 R
2478 6314 0.605589 CCGGGTCCTTTGTTCCAGTC 60.606 60.000 0.00 0.00 0.00 3.51 R
3490 8290 1.202177 GCTGCACATTGTATCAACCCG 60.202 52.381 0.00 0.00 0.00 5.28 R
4607 9836 1.030488 TGCGGAAACCCAAACGACAA 61.030 50.000 0.00 0.00 0.00 3.18 R
6072 12861 1.358152 ACTCCCTCCGTTCCAATCAA 58.642 50.000 0.00 0.00 0.00 2.57 R
7654 30969 0.331278 CACCATTTGGGGTAGCCTCA 59.669 55.000 11.48 4.45 39.79 3.86 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
431 1685 0.318762 GGATGGGACGTCTATCAGCC 59.681 60.000 24.36 21.92 0.00 4.85
726 3731 2.413371 GCAGGAACTTGCACGAATTCTC 60.413 50.000 3.52 0.00 34.60 2.87
836 4050 1.856265 GAGTGCCAAAAGAGGGTGCG 61.856 60.000 0.00 0.00 0.00 5.34
971 4248 3.038280 TGCGGGGAATAATCTTCTCAGA 58.962 45.455 0.00 0.00 0.00 3.27
1133 4425 0.317603 CTCACCGACGACTTCAACGT 60.318 55.000 0.00 0.00 46.58 3.99
1649 5319 5.600696 AGTTAACTTGTTGAAGCCCATTTG 58.399 37.500 1.12 0.00 31.68 2.32
1776 5448 0.887933 ACTACGGGCAAAAATGGCAG 59.112 50.000 4.74 2.99 35.93 4.85
2041 5723 0.531974 ATCAACACTTGTCGCCGTGT 60.532 50.000 0.00 0.00 45.55 4.49
2224 5913 9.722056 GTATCTTGTTGATTGTGGATTATTGAC 57.278 33.333 0.00 0.00 36.65 3.18
2234 5923 4.688879 TGTGGATTATTGACACTGTCGTTC 59.311 41.667 4.71 0.00 34.95 3.95
2478 6314 1.609208 CCTTTCTGTCCCACAGGTTG 58.391 55.000 3.86 0.00 45.94 3.77
2516 6353 5.936372 ACCCGGTAATGACTTAGAACTTTTC 59.064 40.000 0.00 0.00 0.00 2.29
2792 6644 6.793492 AGAATCTTGAGTGTTTGCTACTTC 57.207 37.500 0.00 0.00 0.00 3.01
2799 6651 1.461127 GTGTTTGCTACTTCAGGCTCG 59.539 52.381 0.00 0.00 0.00 5.03
3333 7850 7.535258 GCATTAATTGTTAGAGATATTGCCACG 59.465 37.037 0.00 0.00 0.00 4.94
3404 7921 5.513233 AGTATCACTAACGAGGGTTCCTTA 58.487 41.667 0.00 0.00 37.58 2.69
3702 8505 8.344831 TGTAAAGCATATGCATCTATGTTGTTC 58.655 33.333 28.62 7.82 45.16 3.18
3787 8590 6.149129 TGACCTCTATGCTTACTACATGTG 57.851 41.667 9.11 0.93 0.00 3.21
3982 8838 4.965532 AGGAAGAAGTCACAGCCATAGTAT 59.034 41.667 0.00 0.00 0.00 2.12
4365 9244 1.332178 GTGAGACTGCGTTCTCTTCG 58.668 55.000 13.83 0.00 42.36 3.79
4607 9836 5.047943 GCGTATGATAGAGTAGTGATGGGTT 60.048 44.000 0.00 0.00 0.00 4.11
4858 10438 2.652530 GGCGGTAGTGGTCGTTCA 59.347 61.111 0.00 0.00 0.00 3.18
5088 10680 4.037089 TGGCTATTTATTAGTCGAGACGCA 59.963 41.667 0.00 0.00 35.13 5.24
5655 11391 2.353208 CCTTCTGTCTACACTGTGGAGC 60.353 54.545 15.35 10.75 0.00 4.70
6056 12845 6.793505 GAAATCTAGTTTCTACTCCCTCCA 57.206 41.667 9.29 0.00 42.37 3.86
6057 12846 7.368198 GAAATCTAGTTTCTACTCCCTCCAT 57.632 40.000 9.29 0.00 42.37 3.41
6058 12847 7.757242 AAATCTAGTTTCTACTCCCTCCATT 57.243 36.000 0.00 0.00 35.78 3.16
6059 12848 6.987403 ATCTAGTTTCTACTCCCTCCATTC 57.013 41.667 0.00 0.00 35.78 2.67
6060 12849 5.209659 TCTAGTTTCTACTCCCTCCATTCC 58.790 45.833 0.00 0.00 35.78 3.01
6061 12850 3.803340 AGTTTCTACTCCCTCCATTCCA 58.197 45.455 0.00 0.00 0.00 3.53
6062 12851 4.375313 AGTTTCTACTCCCTCCATTCCAT 58.625 43.478 0.00 0.00 0.00 3.41
6063 12852 5.538877 AGTTTCTACTCCCTCCATTCCATA 58.461 41.667 0.00 0.00 0.00 2.74
6064 12853 6.153924 AGTTTCTACTCCCTCCATTCCATAT 58.846 40.000 0.00 0.00 0.00 1.78
6065 12854 6.621514 AGTTTCTACTCCCTCCATTCCATATT 59.378 38.462 0.00 0.00 0.00 1.28
6066 12855 7.794683 AGTTTCTACTCCCTCCATTCCATATTA 59.205 37.037 0.00 0.00 0.00 0.98
6067 12856 7.554959 TTCTACTCCCTCCATTCCATATTAC 57.445 40.000 0.00 0.00 0.00 1.89
6068 12857 6.630131 TCTACTCCCTCCATTCCATATTACA 58.370 40.000 0.00 0.00 0.00 2.41
6069 12858 7.079700 TCTACTCCCTCCATTCCATATTACAA 58.920 38.462 0.00 0.00 0.00 2.41
6070 12859 6.590656 ACTCCCTCCATTCCATATTACAAA 57.409 37.500 0.00 0.00 0.00 2.83
6071 12860 6.980577 ACTCCCTCCATTCCATATTACAAAA 58.019 36.000 0.00 0.00 0.00 2.44
6072 12861 7.595488 ACTCCCTCCATTCCATATTACAAAAT 58.405 34.615 0.00 0.00 0.00 1.82
6073 12862 8.067488 ACTCCCTCCATTCCATATTACAAAATT 58.933 33.333 0.00 0.00 0.00 1.82
6074 12863 8.248904 TCCCTCCATTCCATATTACAAAATTG 57.751 34.615 0.00 0.00 0.00 2.32
6075 12864 8.064389 TCCCTCCATTCCATATTACAAAATTGA 58.936 33.333 0.00 0.00 0.00 2.57
6076 12865 8.873144 CCCTCCATTCCATATTACAAAATTGAT 58.127 33.333 0.00 0.00 0.00 2.57
6083 12872 9.579768 TTCCATATTACAAAATTGATTGGAACG 57.420 29.630 0.00 0.00 36.01 3.95
6084 12873 8.194104 TCCATATTACAAAATTGATTGGAACGG 58.806 33.333 0.00 0.00 36.01 4.44
6085 12874 8.194104 CCATATTACAAAATTGATTGGAACGGA 58.806 33.333 0.00 0.00 36.01 4.69
6086 12875 9.236691 CATATTACAAAATTGATTGGAACGGAG 57.763 33.333 0.00 0.00 36.01 4.63
6087 12876 4.519540 ACAAAATTGATTGGAACGGAGG 57.480 40.909 0.00 0.00 34.56 4.30
6088 12877 3.258123 ACAAAATTGATTGGAACGGAGGG 59.742 43.478 0.00 0.00 34.56 4.30
6089 12878 3.449746 AAATTGATTGGAACGGAGGGA 57.550 42.857 0.00 0.00 0.00 4.20
6090 12879 2.717639 ATTGATTGGAACGGAGGGAG 57.282 50.000 0.00 0.00 0.00 4.30
6091 12880 1.358152 TTGATTGGAACGGAGGGAGT 58.642 50.000 0.00 0.00 0.00 3.85
6092 12881 2.241281 TGATTGGAACGGAGGGAGTA 57.759 50.000 0.00 0.00 0.00 2.59
6108 12897 6.296145 GGAGGGAGTATAAGATTGATTGGGAG 60.296 46.154 0.00 0.00 0.00 4.30
6250 13041 2.619013 ACAATGCAAGAGCGCTTAAC 57.381 45.000 13.26 0.00 46.23 2.01
6338 13129 2.272797 AGGAGCGCCTACTCGAGT 59.727 61.111 23.66 23.66 44.74 4.18
6359 13150 6.625310 CGAGTGCTAATCTAATTCTTTTTCGC 59.375 38.462 0.00 0.00 0.00 4.70
6377 13170 2.014128 CGCGTGGGAAAAATGGATAGT 58.986 47.619 0.00 0.00 0.00 2.12
6434 13228 4.412933 CGCCCGATCGCTAGAAAA 57.587 55.556 10.32 0.00 0.00 2.29
6488 13282 2.651382 GGATTTACCCATAACGGCCT 57.349 50.000 0.00 0.00 0.00 5.19
6505 13299 2.772739 CTGGACTTGAATCCTGGCG 58.227 57.895 0.00 0.00 39.75 5.69
6549 13343 1.148310 CATGCCCTTAATACGCTCCG 58.852 55.000 0.00 0.00 0.00 4.63
6576 13370 3.149196 GCAAGGAAACTGAGTGGATGAA 58.851 45.455 0.00 0.00 42.68 2.57
6690 13484 1.009060 TGGCCTTGTATACTCCCTCCA 59.991 52.381 3.32 2.87 0.00 3.86
6852 13661 4.024048 CCAAACAAGACATGTAGTGGTCAC 60.024 45.833 0.00 0.00 42.99 3.67
6857 13666 4.258702 AGACATGTAGTGGTCACTTCAC 57.741 45.455 9.02 3.31 40.62 3.18
6907 13716 9.590088 AAATAAATGTTACGTTCTCTCGTTTTC 57.410 29.630 0.00 0.00 43.80 2.29
7060 13875 6.673839 AGGCTACTTATCTTACTTCATCCC 57.326 41.667 0.00 0.00 0.00 3.85
7210 14039 4.494484 TGAGACTATCAAACACGACATGG 58.506 43.478 0.00 0.00 34.02 3.66
7219 14048 3.478857 AACACGACATGGAGTGGTTAA 57.521 42.857 21.41 0.00 42.25 2.01
7286 14116 3.849563 TTCGTTTTCCCTTCTCCTTGA 57.150 42.857 0.00 0.00 0.00 3.02
7324 14154 8.095452 ACCTAAGATGACTTATTCACTTGGAT 57.905 34.615 0.00 0.00 36.92 3.41
7385 14216 8.958043 GCAGAGTAATGAGTTTAGTTTGTTTTG 58.042 33.333 0.00 0.00 31.21 2.44
7481 30796 0.799917 CGTCGATCAGTGCACCAGAG 60.800 60.000 14.63 1.20 0.00 3.35
7489 30804 1.673665 GTGCACCAGAGAGCCCAAG 60.674 63.158 5.22 0.00 0.00 3.61
7597 30912 0.251073 GCCGGTTGCTCCCTTACTTA 59.749 55.000 1.90 0.00 36.87 2.24
7740 31055 3.471680 AGCTCTTTCACTTCCTTGTGAC 58.528 45.455 0.00 0.00 45.32 3.67
7781 31110 2.603560 CGCCTAAGAACTTCCAATCGAC 59.396 50.000 0.00 0.00 0.00 4.20
7825 31155 4.789012 AACTGTAATTGCCCATGTTGAG 57.211 40.909 0.00 0.00 0.00 3.02
7893 31708 5.863935 TGTCGTCAGAGAAGATATTGTTGTG 59.136 40.000 0.00 0.00 0.00 3.33
7896 31711 5.349817 CGTCAGAGAAGATATTGTTGTGCTT 59.650 40.000 0.00 0.00 0.00 3.91
7909 31724 3.186909 GTTGTGCTTCAAAACCTGAACC 58.813 45.455 0.00 0.00 39.20 3.62
7919 31734 5.640147 TCAAAACCTGAACCCTATGACATT 58.360 37.500 0.00 0.00 0.00 2.71
7972 31787 5.921962 TCATCATGATAATACTCCCTCCG 57.078 43.478 8.15 0.00 0.00 4.63
7989 31804 4.383335 CCCTCCGTTTACTTATACAAGGCA 60.383 45.833 0.00 0.00 35.97 4.75
7992 31807 5.549347 TCCGTTTACTTATACAAGGCAACA 58.451 37.500 0.00 0.00 35.97 3.33
8064 31880 9.922305 GAGACAAAAGTTAATGATAATTCCTCG 57.078 33.333 0.00 0.00 0.00 4.63
8075 31891 5.972935 TGATAATTCCTCGAACTAGCAACA 58.027 37.500 0.00 0.00 0.00 3.33
8185 32001 6.921914 TCCCACTAAACAAAAAGAAAAACGA 58.078 32.000 0.00 0.00 0.00 3.85
8268 32084 9.535170 CTTGTATATAGAAATGGAGGGAGTAGA 57.465 37.037 0.00 0.00 0.00 2.59
8312 32128 9.087871 TCCCTTTTTATGAATCAGATTTGTCAA 57.912 29.630 0.00 0.00 0.00 3.18
8446 32287 2.549082 TCACCGTTCCCCACCTAATTA 58.451 47.619 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
431 1685 1.609501 TCCCTCCTCCGTGAACCTG 60.610 63.158 0.00 0.00 0.00 4.00
495 1749 1.678635 CAGCCCCAGCGAAATTCCA 60.679 57.895 0.00 0.00 46.67 3.53
971 4248 2.577059 CCTACCGCGGTGTGATGT 59.423 61.111 40.02 14.70 0.00 3.06
1649 5319 1.199097 CCACGTGTGCTGTAATTTCCC 59.801 52.381 15.65 0.00 0.00 3.97
2194 5883 5.565592 TCCACAATCAACAAGATACATGC 57.434 39.130 0.00 0.00 35.39 4.06
2224 5913 1.442769 CCTGATTGGGAACGACAGTG 58.557 55.000 0.00 0.00 0.00 3.66
2478 6314 0.605589 CCGGGTCCTTTGTTCCAGTC 60.606 60.000 0.00 0.00 0.00 3.51
2549 6386 7.062255 GCAAACTACTTGAATAAAGAATGGCAC 59.938 37.037 0.00 0.00 39.38 5.01
2781 6633 1.797025 ACGAGCCTGAAGTAGCAAAC 58.203 50.000 0.00 0.00 0.00 2.93
2792 6644 1.078759 CAGCTTTCCGTACGAGCCTG 61.079 60.000 18.76 13.16 37.11 4.85
2799 6651 3.617263 CACCAAGTATCAGCTTTCCGTAC 59.383 47.826 0.00 0.00 0.00 3.67
3124 7028 2.192664 ATATTGCACGGTCACACCAA 57.807 45.000 0.00 0.00 38.47 3.67
3133 7037 6.198687 CACTTTGGTATGTTATATTGCACGG 58.801 40.000 0.00 0.00 0.00 4.94
3374 7891 6.803642 ACCCTCGTTAGTGATACTATGTTTC 58.196 40.000 0.00 0.00 29.64 2.78
3490 8290 1.202177 GCTGCACATTGTATCAACCCG 60.202 52.381 0.00 0.00 0.00 5.28
3808 8611 4.461198 ACAAACTTTTGGCAGCTAGTACT 58.539 39.130 0.00 0.00 42.34 2.73
3982 8838 5.183713 CCTACATGATGCAAACTTCTTTCCA 59.816 40.000 0.00 0.00 0.00 3.53
4365 9244 1.080974 GGCAGCACAGCAACACATC 60.081 57.895 0.00 0.00 35.83 3.06
4607 9836 1.030488 TGCGGAAACCCAAACGACAA 61.030 50.000 0.00 0.00 0.00 3.18
4703 10052 7.027161 GCCGTTTAATAAGTGTTGTCAATCAT 58.973 34.615 0.00 0.00 0.00 2.45
4821 10392 1.153765 TCAGAACGAGCTGCCGATG 60.154 57.895 15.53 11.10 35.86 3.84
4822 10393 1.153745 GTCAGAACGAGCTGCCGAT 60.154 57.895 15.53 5.44 35.86 4.18
4858 10438 2.060050 ATCGAGATTCCGAGACCACT 57.940 50.000 0.00 0.00 42.21 4.00
5088 10680 5.536916 TGATTTTACGGTCCTTTGGTCATTT 59.463 36.000 0.00 0.00 0.00 2.32
5258 10856 6.763715 AAATGGCCAGAGATAGGTTACATA 57.236 37.500 13.05 0.00 0.00 2.29
5329 10977 5.479375 AGTCATGCATTTTTCCTCTCAATGT 59.521 36.000 0.00 0.00 31.60 2.71
5655 11391 2.632377 ACCAGAGTAAATGCATGGACG 58.368 47.619 0.00 0.00 34.99 4.79
6048 12837 8.362639 CAATTTTGTAATATGGAATGGAGGGAG 58.637 37.037 0.00 0.00 0.00 4.30
6049 12838 8.064389 TCAATTTTGTAATATGGAATGGAGGGA 58.936 33.333 0.00 0.00 0.00 4.20
6050 12839 8.248904 TCAATTTTGTAATATGGAATGGAGGG 57.751 34.615 0.00 0.00 0.00 4.30
6057 12846 9.579768 CGTTCCAATCAATTTTGTAATATGGAA 57.420 29.630 0.00 0.00 0.00 3.53
6058 12847 8.194104 CCGTTCCAATCAATTTTGTAATATGGA 58.806 33.333 0.00 0.00 0.00 3.41
6059 12848 8.194104 TCCGTTCCAATCAATTTTGTAATATGG 58.806 33.333 0.00 0.00 0.00 2.74
6060 12849 9.236691 CTCCGTTCCAATCAATTTTGTAATATG 57.763 33.333 0.00 0.00 0.00 1.78
6061 12850 8.413229 CCTCCGTTCCAATCAATTTTGTAATAT 58.587 33.333 0.00 0.00 0.00 1.28
6062 12851 7.147983 CCCTCCGTTCCAATCAATTTTGTAATA 60.148 37.037 0.00 0.00 0.00 0.98
6063 12852 6.350949 CCCTCCGTTCCAATCAATTTTGTAAT 60.351 38.462 0.00 0.00 0.00 1.89
6064 12853 5.047660 CCCTCCGTTCCAATCAATTTTGTAA 60.048 40.000 0.00 0.00 0.00 2.41
6065 12854 4.461081 CCCTCCGTTCCAATCAATTTTGTA 59.539 41.667 0.00 0.00 0.00 2.41
6066 12855 3.258123 CCCTCCGTTCCAATCAATTTTGT 59.742 43.478 0.00 0.00 0.00 2.83
6067 12856 3.509575 TCCCTCCGTTCCAATCAATTTTG 59.490 43.478 0.00 0.00 0.00 2.44
6068 12857 3.763897 CTCCCTCCGTTCCAATCAATTTT 59.236 43.478 0.00 0.00 0.00 1.82
6069 12858 3.245264 ACTCCCTCCGTTCCAATCAATTT 60.245 43.478 0.00 0.00 0.00 1.82
6070 12859 2.308866 ACTCCCTCCGTTCCAATCAATT 59.691 45.455 0.00 0.00 0.00 2.32
6071 12860 1.916181 ACTCCCTCCGTTCCAATCAAT 59.084 47.619 0.00 0.00 0.00 2.57
6072 12861 1.358152 ACTCCCTCCGTTCCAATCAA 58.642 50.000 0.00 0.00 0.00 2.57
6073 12862 2.241281 TACTCCCTCCGTTCCAATCA 57.759 50.000 0.00 0.00 0.00 2.57
6074 12863 4.587684 TCTTATACTCCCTCCGTTCCAATC 59.412 45.833 0.00 0.00 0.00 2.67
6075 12864 4.553678 TCTTATACTCCCTCCGTTCCAAT 58.446 43.478 0.00 0.00 0.00 3.16
6076 12865 3.985127 TCTTATACTCCCTCCGTTCCAA 58.015 45.455 0.00 0.00 0.00 3.53
6077 12866 3.675348 TCTTATACTCCCTCCGTTCCA 57.325 47.619 0.00 0.00 0.00 3.53
6078 12867 4.587684 TCAATCTTATACTCCCTCCGTTCC 59.412 45.833 0.00 0.00 0.00 3.62
6079 12868 5.786264 TCAATCTTATACTCCCTCCGTTC 57.214 43.478 0.00 0.00 0.00 3.95
6080 12869 6.464465 CCAATCAATCTTATACTCCCTCCGTT 60.464 42.308 0.00 0.00 0.00 4.44
6081 12870 5.012148 CCAATCAATCTTATACTCCCTCCGT 59.988 44.000 0.00 0.00 0.00 4.69
6082 12871 5.482908 CCAATCAATCTTATACTCCCTCCG 58.517 45.833 0.00 0.00 0.00 4.63
6083 12872 5.548056 TCCCAATCAATCTTATACTCCCTCC 59.452 44.000 0.00 0.00 0.00 4.30
6084 12873 6.498651 TCTCCCAATCAATCTTATACTCCCTC 59.501 42.308 0.00 0.00 0.00 4.30
6085 12874 6.393897 TCTCCCAATCAATCTTATACTCCCT 58.606 40.000 0.00 0.00 0.00 4.20
6086 12875 6.688073 TCTCCCAATCAATCTTATACTCCC 57.312 41.667 0.00 0.00 0.00 4.30
6087 12876 7.993183 TGTTTCTCCCAATCAATCTTATACTCC 59.007 37.037 0.00 0.00 0.00 3.85
6088 12877 8.964476 TGTTTCTCCCAATCAATCTTATACTC 57.036 34.615 0.00 0.00 0.00 2.59
6089 12878 8.552296 ACTGTTTCTCCCAATCAATCTTATACT 58.448 33.333 0.00 0.00 0.00 2.12
6090 12879 8.738645 ACTGTTTCTCCCAATCAATCTTATAC 57.261 34.615 0.00 0.00 0.00 1.47
6091 12880 7.993183 GGACTGTTTCTCCCAATCAATCTTATA 59.007 37.037 0.00 0.00 0.00 0.98
6092 12881 6.830838 GGACTGTTTCTCCCAATCAATCTTAT 59.169 38.462 0.00 0.00 0.00 1.73
6250 13041 4.900635 ATTTTATTGTCTAAGCGCCTGG 57.099 40.909 2.29 0.00 0.00 4.45
6335 13126 6.625310 CGCGAAAAAGAATTAGATTAGCACTC 59.375 38.462 0.00 0.00 0.00 3.51
6338 13129 6.247903 CACGCGAAAAAGAATTAGATTAGCA 58.752 36.000 15.93 0.00 0.00 3.49
6359 13150 3.016736 AGCACTATCCATTTTTCCCACG 58.983 45.455 0.00 0.00 0.00 4.94
6434 13228 1.514678 TTTTCGCTGGCGTTGATGCT 61.515 50.000 14.55 0.00 40.74 3.79
6440 13234 0.521735 GAAGGATTTTCGCTGGCGTT 59.478 50.000 14.55 0.00 40.74 4.84
6488 13282 1.377202 GCGCCAGGATTCAAGTCCA 60.377 57.895 0.00 0.00 40.90 4.02
6521 13315 2.483014 TTAAGGGCATGTACAACGCT 57.517 45.000 17.26 14.45 0.00 5.07
6549 13343 1.610522 ACTCAGTTTCCTTGCATGCAC 59.389 47.619 22.58 7.85 0.00 4.57
6576 13370 4.308899 GTCATAATGACAGTCGGCTACT 57.691 45.455 0.00 0.00 46.22 2.57
6606 13400 7.803279 ACTAGCAACCTATTTAATACTTGCC 57.197 36.000 14.29 3.47 35.63 4.52
6799 13593 2.505819 AGACGCCCCACATCTCTTATTT 59.494 45.455 0.00 0.00 0.00 1.40
6907 13716 1.742768 CGCTACTAAGGCAGAGGGG 59.257 63.158 0.00 0.00 0.00 4.79
6986 13795 8.217111 TCATTCATTTATACAAGGCCACTATGA 58.783 33.333 5.01 0.00 0.00 2.15
7007 13816 8.739972 ACCAAAAACATAGTACTCCATTCATTC 58.260 33.333 0.00 0.00 0.00 2.67
7266 14095 3.849563 TCAAGGAGAAGGGAAAACGAA 57.150 42.857 0.00 0.00 0.00 3.85
7324 14154 5.461516 TTGACTACATAGTACTCCCTCCA 57.538 43.478 0.00 0.00 36.50 3.86
7489 30804 2.356793 CATCATCTCGGGCGGCTC 60.357 66.667 9.56 0.00 0.00 4.70
7597 30912 1.749638 AGTGCTAGTAGGCGCGTCT 60.750 57.895 20.79 20.79 45.99 4.18
7654 30969 0.331278 CACCATTTGGGGTAGCCTCA 59.669 55.000 11.48 4.45 39.79 3.86
7740 31055 4.148891 GCGAACATCGTTTTGACTAAAGG 58.851 43.478 1.45 0.00 42.81 3.11
7781 31110 3.792716 GGCAACCAAACATCCTTCG 57.207 52.632 0.00 0.00 0.00 3.79
7825 31155 3.181497 CCAATCCGACACAATCAATCCAC 60.181 47.826 0.00 0.00 0.00 4.02
7896 31711 4.715534 TGTCATAGGGTTCAGGTTTTGA 57.284 40.909 0.00 0.00 0.00 2.69
7972 31787 9.685828 TTTCATTGTTGCCTTGTATAAGTAAAC 57.314 29.630 0.00 3.54 32.32 2.01
8003 31818 5.123227 GTGGCCTTGTATAGATGCAAAGTA 58.877 41.667 3.32 0.00 32.12 2.24
8070 31886 7.697352 TGCATGCAAGTATTAAATATGTTGC 57.303 32.000 20.30 8.37 37.73 4.17
8268 32084 3.967987 AGGGATCTTACATTCCTACGCTT 59.032 43.478 0.00 0.00 32.34 4.68
8312 32128 7.820044 ACAAAATCGTGTTTGTTTGTAACAT 57.180 28.000 11.67 0.00 46.97 2.71
8487 32334 6.662755 TCAGGTATCCTAAACTCAATTGCAT 58.337 36.000 0.00 0.00 29.64 3.96
8509 32356 1.474478 TGCGAGCAAAAACTTGGTTCA 59.526 42.857 0.00 0.00 32.16 3.18
8579 32426 1.814793 GAGCAAAGGAGGAGTTGGTC 58.185 55.000 0.45 0.45 42.85 4.02


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

AutoCloner maintained by Alex Coulton.