Multiple sequence alignment - TraesCS5D01G290800

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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 TraesCS5D01G290800 chr5D 100.000 7679 0 0 1 7679 388602780 388595102 0.000000e+00 14181.0
1 TraesCS5D01G290800 chr5D 88.944 1800 116 27 2752 4523 353968163 353966419 0.000000e+00 2145.0
2 TraesCS5D01G290800 chr5D 85.027 1663 153 51 4337 5949 353970397 353968781 0.000000e+00 1604.0
3 TraesCS5D01G290800 chr5D 87.425 1169 90 20 3202 4336 353971577 353970432 0.000000e+00 1291.0
4 TraesCS5D01G290800 chr5D 84.012 1301 120 33 4671 5953 388384084 388382854 0.000000e+00 1170.0
5 TraesCS5D01G290800 chr5D 94.213 743 38 3 4560 5302 353959776 353959039 0.000000e+00 1129.0
6 TraesCS5D01G290800 chr5D 86.243 1054 82 22 3314 4336 388385515 388384494 0.000000e+00 1085.0
7 TraesCS5D01G290800 chr5D 90.566 530 37 7 6059 6588 353968720 353968204 0.000000e+00 689.0
8 TraesCS5D01G290800 chr5D 90.588 425 31 3 6059 6477 388382860 388382439 8.710000e-154 555.0
9 TraesCS5D01G290800 chr5D 92.857 350 19 6 6470 6815 353955364 353955017 3.200000e-138 503.0
10 TraesCS5D01G290800 chr5D 93.168 322 19 3 4337 4655 388384391 388384070 3.240000e-128 470.0
11 TraesCS5D01G290800 chr5D 88.798 366 27 10 2847 3208 388385896 388385541 3.290000e-118 436.0
12 TraesCS5D01G290800 chr5D 85.430 453 27 17 6059 6476 353955971 353955523 1.180000e-117 435.0
13 TraesCS5D01G290800 chr5D 87.834 337 31 3 2719 3049 353950090 353949758 3.360000e-103 387.0
14 TraesCS5D01G290800 chr5D 84.000 325 30 14 490 797 484667966 484668285 7.540000e-75 292.0
15 TraesCS5D01G290800 chr5D 86.617 269 26 7 490 749 484705039 484705306 9.750000e-74 289.0
16 TraesCS5D01G290800 chr5D 82.545 275 28 5 6543 6809 388382417 388382155 2.790000e-54 224.0
17 TraesCS5D01G290800 chr5D 87.387 111 11 2 6707 6815 386959745 386959636 2.910000e-24 124.0
18 TraesCS5D01G290800 chr5D 100.000 31 0 0 5379 5409 388597266 388597236 2.990000e-04 58.4
19 TraesCS5D01G290800 chr5D 100.000 31 0 0 5515 5545 388597402 388597372 2.990000e-04 58.4
20 TraesCS5D01G290800 chr5B 89.348 4309 288 74 2394 6660 467025217 467021038 0.000000e+00 5256.0
21 TraesCS5D01G290800 chr5B 86.957 552 25 17 796 1328 488711800 488711277 1.860000e-160 577.0
22 TraesCS5D01G290800 chr5B 85.375 506 28 13 328 797 467025709 467025214 4.170000e-132 483.0
23 TraesCS5D01G290800 chr5B 89.200 250 24 2 2427 2676 596513576 596513330 7.480000e-80 309.0
24 TraesCS5D01G290800 chr5B 85.424 295 27 8 2427 2718 596500179 596499898 7.540000e-75 292.0
25 TraesCS5D01G290800 chr5B 91.351 185 9 5 2 182 467026030 467025849 5.950000e-61 246.0
26 TraesCS5D01G290800 chr5B 82.812 256 40 4 2152 2405 375414418 375414671 7.750000e-55 226.0
27 TraesCS5D01G290800 chr5A 94.427 3212 92 27 3453 6630 491588767 491585609 0.000000e+00 4859.0
28 TraesCS5D01G290800 chr5A 88.245 1863 125 32 2837 4655 491573595 491571783 0.000000e+00 2141.0
29 TraesCS5D01G290800 chr5A 92.718 1030 58 8 2394 3419 491589785 491588769 0.000000e+00 1471.0
30 TraesCS5D01G290800 chr5A 91.106 877 64 3 6816 7679 113804988 113805863 0.000000e+00 1175.0
31 TraesCS5D01G290800 chr5A 88.951 896 67 9 6816 7679 634632320 634631425 0.000000e+00 1077.0
32 TraesCS5D01G290800 chr5A 88.603 895 69 11 6816 7679 552236072 552236964 0.000000e+00 1057.0
33 TraesCS5D01G290800 chr5A 91.654 647 33 7 4671 5296 491571797 491571151 0.000000e+00 876.0
34 TraesCS5D01G290800 chr5A 87.703 553 27 10 794 1328 650516325 650515796 2.370000e-169 606.0
35 TraesCS5D01G290800 chr5A 89.976 419 33 4 6065 6477 491570841 491570426 4.080000e-147 532.0
36 TraesCS5D01G290800 chr5A 93.671 316 12 4 490 797 491590097 491589782 4.200000e-127 466.0
37 TraesCS5D01G290800 chr5A 86.392 316 35 8 5637 5950 491571153 491570844 9.550000e-89 339.0
38 TraesCS5D01G290800 chr5A 91.209 182 15 1 2 182 491590904 491590723 5.950000e-61 246.0
39 TraesCS5D01G290800 chr5A 81.597 288 26 9 6543 6815 491570404 491570129 6.040000e-51 213.0
40 TraesCS5D01G290800 chr5A 84.375 224 24 8 264 478 491590369 491590148 7.810000e-50 209.0
41 TraesCS5D01G290800 chr5A 100.000 31 0 0 5515 5545 491586830 491586800 2.990000e-04 58.4
42 TraesCS5D01G290800 chr4B 92.151 1083 48 7 3561 4619 31869370 31870439 0.000000e+00 1495.0
43 TraesCS5D01G290800 chr4B 89.089 1164 88 15 4604 5756 31870453 31871588 0.000000e+00 1410.0
44 TraesCS5D01G290800 chr4B 92.404 882 58 3 2683 3563 31866434 31867307 0.000000e+00 1249.0
45 TraesCS5D01G290800 chr4B 87.456 845 85 9 4831 5667 356000152 356000983 0.000000e+00 953.0
46 TraesCS5D01G290800 chr4B 85.714 616 57 15 6059 6651 31871806 31872413 8.460000e-174 621.0
47 TraesCS5D01G290800 chr4B 95.251 358 17 0 1175 1532 160224454 160224097 1.120000e-157 568.0
48 TraesCS5D01G290800 chr4B 86.747 166 14 2 5230 5387 581609469 581609304 2.200000e-40 178.0
49 TraesCS5D01G290800 chr7D 91.572 878 58 6 6816 7679 525763821 525762946 0.000000e+00 1197.0
50 TraesCS5D01G290800 chr7D 95.464 485 20 1 1175 1659 47977596 47977114 0.000000e+00 773.0
51 TraesCS5D01G290800 chr7D 92.688 506 23 5 1894 2397 47960891 47960398 0.000000e+00 717.0
52 TraesCS5D01G290800 chr7D 88.629 299 31 3 2427 2723 104891031 104891328 2.040000e-95 361.0
53 TraesCS5D01G290800 chr7D 83.587 329 25 15 490 794 104890665 104890988 1.630000e-71 281.0
54 TraesCS5D01G290800 chr7D 94.444 90 4 1 1804 1892 47977066 47976977 3.740000e-28 137.0
55 TraesCS5D01G290800 chr4D 91.250 880 58 5 6816 7679 488872707 488871831 0.000000e+00 1181.0
56 TraesCS5D01G290800 chr4D 96.289 485 16 1 1175 1659 315359852 315360334 0.000000e+00 795.0
57 TraesCS5D01G290800 chr4D 94.643 504 20 3 1894 2397 424550504 424550008 0.000000e+00 774.0
58 TraesCS5D01G290800 chr4D 93.849 504 24 3 1894 2397 315360518 315361014 0.000000e+00 752.0
59 TraesCS5D01G290800 chr4D 98.039 204 2 1 1456 1659 424550889 424550688 3.410000e-93 353.0
60 TraesCS5D01G290800 chr4D 96.591 88 3 0 1805 1892 315360384 315360471 6.210000e-31 147.0
61 TraesCS5D01G290800 chr4D 94.444 90 4 1 1804 1892 424550640 424550551 3.740000e-28 137.0
62 TraesCS5D01G290800 chr4D 87.952 83 8 2 2642 2722 370031087 370031005 6.340000e-16 97.1
63 TraesCS5D01G290800 chr4D 87.671 73 6 2 2653 2722 394380680 394380608 1.780000e-11 82.4
64 TraesCS5D01G290800 chr1B 91.210 876 61 3 6816 7679 548682306 548683177 0.000000e+00 1177.0
65 TraesCS5D01G290800 chr1B 89.640 888 63 10 6807 7679 539843671 539844544 0.000000e+00 1103.0
66 TraesCS5D01G290800 chr1B 95.251 358 17 0 1175 1532 204550903 204551260 1.120000e-157 568.0
67 TraesCS5D01G290800 chr1B 90.314 382 29 1 2024 2397 58874924 58874543 1.930000e-135 494.0
68 TraesCS5D01G290800 chr1B 83.150 546 49 15 795 1321 58984402 58983881 7.020000e-125 459.0
69 TraesCS5D01G290800 chr1B 96.078 51 2 0 4094 4144 426712 426662 4.940000e-12 84.2
70 TraesCS5D01G290800 chr4A 83.692 1300 133 33 4671 5953 45874151 45872914 0.000000e+00 1153.0
71 TraesCS5D01G290800 chr4A 85.998 857 62 22 3505 4336 45875313 45874490 0.000000e+00 865.0
72 TraesCS5D01G290800 chr4A 87.435 573 32 19 774 1328 702024868 702024318 2.350000e-174 623.0
73 TraesCS5D01G290800 chr4A 90.610 426 29 5 6059 6477 45872920 45872499 8.710000e-154 555.0
74 TraesCS5D01G290800 chr4A 88.889 414 29 5 2970 3383 45875704 45875308 1.930000e-135 494.0
75 TraesCS5D01G290800 chr4A 92.812 320 21 2 4337 4655 45874455 45874137 5.430000e-126 462.0
76 TraesCS5D01G290800 chr4A 83.916 286 22 7 6543 6815 45872477 45872203 1.280000e-62 252.0
77 TraesCS5D01G290800 chr4A 94.937 79 3 1 1804 1881 255810511 255810433 1.050000e-23 122.0
78 TraesCS5D01G290800 chr4A 100.000 33 0 0 2394 2426 452349730 452349698 2.310000e-05 62.1
79 TraesCS5D01G290800 chr6D 90.568 880 66 5 6815 7679 45803624 45802747 0.000000e+00 1149.0
80 TraesCS5D01G290800 chr6D 92.476 319 16 4 1941 2259 445128721 445128411 4.230000e-122 449.0
81 TraesCS5D01G290800 chr6D 93.684 95 5 1 4562 4655 65465554 65465460 2.890000e-29 141.0
82 TraesCS5D01G290800 chr3B 90.422 877 65 5 6816 7679 575281031 575280161 0.000000e+00 1136.0
83 TraesCS5D01G290800 chr3B 89.180 878 69 11 6815 7679 13523513 13522649 0.000000e+00 1072.0
84 TraesCS5D01G290800 chr3B 87.086 573 33 20 774 1328 756616398 756616947 1.830000e-170 610.0
85 TraesCS5D01G290800 chr3B 93.548 155 10 0 2245 2399 143598539 143598693 1.670000e-56 231.0
86 TraesCS5D01G290800 chr2B 90.158 884 54 7 6816 7679 80544140 80545010 0.000000e+00 1120.0
87 TraesCS5D01G290800 chr2B 95.531 358 16 0 1175 1532 729785950 729785593 2.400000e-159 573.0
88 TraesCS5D01G290800 chr2B 86.984 315 18 13 502 797 552434523 552434213 4.440000e-87 333.0
89 TraesCS5D01G290800 chr2B 85.149 303 35 8 2427 2726 97941220 97941515 1.250000e-77 302.0
90 TraesCS5D01G290800 chr2B 94.595 74 4 0 1808 1881 729783006 729782933 1.750000e-21 115.0
91 TraesCS5D01G290800 chr2B 96.970 33 1 0 2394 2426 97941173 97941205 1.000000e-03 56.5
92 TraesCS5D01G290800 chr7A 89.286 896 64 11 6815 7679 689944317 689943423 0.000000e+00 1094.0
93 TraesCS5D01G290800 chr7A 88.294 299 33 2 2427 2723 109343286 109343584 2.640000e-94 357.0
94 TraesCS5D01G290800 chr7A 84.211 323 29 8 490 795 109342927 109343244 2.100000e-75 294.0
95 TraesCS5D01G290800 chr7A 93.671 79 4 1 1804 1881 50903618 50903540 4.870000e-22 117.0
96 TraesCS5D01G290800 chr7A 100.000 32 0 0 2395 2426 109343240 109343271 8.320000e-05 60.2
97 TraesCS5D01G290800 chr6B 90.824 752 55 3 6816 7554 130318471 130319221 0.000000e+00 994.0
98 TraesCS5D01G290800 chr6B 95.833 48 2 0 264 311 320399666 320399713 2.300000e-10 78.7
99 TraesCS5D01G290800 chr6A 86.425 884 97 6 6816 7679 117579894 117579014 0.000000e+00 946.0
100 TraesCS5D01G290800 chr6A 87.260 573 33 18 774 1328 116952430 116951880 1.090000e-172 617.0
101 TraesCS5D01G290800 chr6A 87.681 552 28 10 795 1328 143073650 143074179 2.370000e-169 606.0
102 TraesCS5D01G290800 chr3D 97.938 485 8 1 1175 1659 21411366 21410884 0.000000e+00 839.0
103 TraesCS5D01G290800 chr3D 97.732 485 9 1 1175 1659 21433912 21433430 0.000000e+00 833.0
104 TraesCS5D01G290800 chr3D 94.643 504 23 2 1894 2397 592848891 592848392 0.000000e+00 778.0
105 TraesCS5D01G290800 chr3D 95.670 485 19 1 1175 1659 592849557 592849075 0.000000e+00 778.0
106 TraesCS5D01G290800 chr3D 96.447 394 12 1 2004 2397 21408229 21407838 0.000000e+00 649.0
107 TraesCS5D01G290800 chr3D 84.314 612 68 21 795 1395 92856655 92856061 2.400000e-159 573.0
108 TraesCS5D01G290800 chr3D 85.765 281 33 7 4803 5082 99195172 99194898 2.710000e-74 291.0
109 TraesCS5D01G290800 chr3D 80.150 267 38 8 2394 2646 581730407 581730672 1.320000e-42 185.0
110 TraesCS5D01G290800 chr3D 84.768 151 15 4 4671 4814 99195381 99195232 2.230000e-30 145.0
111 TraesCS5D01G290800 chr3D 95.556 90 3 1 1804 1892 592849027 592848938 8.030000e-30 143.0
112 TraesCS5D01G290800 chr3D 91.667 48 4 0 264 311 500884769 500884722 4.970000e-07 67.6
113 TraesCS5D01G290800 chr3D 97.143 35 1 0 6004 6038 386725974 386726008 8.320000e-05 60.2
114 TraesCS5D01G290800 chr2D 97.320 485 11 1 1175 1659 179878039 179877557 0.000000e+00 822.0
115 TraesCS5D01G290800 chr2D 95.040 504 20 2 1894 2397 179877373 179876875 0.000000e+00 787.0
116 TraesCS5D01G290800 chr2D 94.257 505 22 3 1894 2397 603008079 603008577 0.000000e+00 765.0
117 TraesCS5D01G290800 chr2D 88.065 310 21 10 502 795 473101121 473100812 3.410000e-93 353.0
118 TraesCS5D01G290800 chr2D 88.294 299 22 4 2427 2717 473100763 473100470 5.700000e-91 346.0
119 TraesCS5D01G290800 chr2D 85.479 303 34 8 2427 2726 62386886 62387181 2.690000e-79 307.0
120 TraesCS5D01G290800 chr2D 85.484 310 25 13 503 793 62386533 62386841 9.680000e-79 305.0
121 TraesCS5D01G290800 chr2D 95.556 90 3 1 1804 1892 179877509 179877420 8.030000e-30 143.0
122 TraesCS5D01G290800 chr2D 95.294 85 4 0 1808 1892 603007948 603008032 1.340000e-27 135.0
123 TraesCS5D01G290800 chr2D 93.750 48 2 1 5994 6040 522526146 522526099 3.840000e-08 71.3
124 TraesCS5D01G290800 chr2D 96.970 33 1 0 2394 2426 62386839 62386871 1.000000e-03 56.5
125 TraesCS5D01G290800 chr2A 87.050 556 31 11 791 1328 631847369 631847901 2.390000e-164 590.0
126 TraesCS5D01G290800 chr2A 95.833 264 7 2 2136 2397 631847885 631848146 2.560000e-114 424.0
127 TraesCS5D01G290800 chr2A 85.852 311 24 13 502 793 63303110 63302801 5.790000e-81 313.0
128 TraesCS5D01G290800 chr2A 87.451 255 24 6 2477 2726 614584566 614584315 3.510000e-73 287.0
129 TraesCS5D01G290800 chr2A 100.000 32 0 0 2395 2426 614584646 614584615 8.320000e-05 60.2
130 TraesCS5D01G290800 chr7B 86.243 189 23 3 1 186 524710505 524710317 1.310000e-47 202.0
131 TraesCS5D01G290800 chr7B 80.741 270 36 8 2394 2648 745062219 745062487 6.080000e-46 196.0
132 TraesCS5D01G290800 chr7B 96.000 50 2 0 264 313 538369541 538369492 1.780000e-11 82.4
133 TraesCS5D01G290800 chr1D 89.286 112 11 1 4671 4782 450715305 450715195 1.040000e-28 139.0
134 TraesCS5D01G290800 chr1A 86.735 98 9 4 3773 3870 574801421 574801514 1.050000e-18 106.0


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 TraesCS5D01G290800 chr5D 388595102 388602780 7678 True 14181.000000 14181 100.000000 1 7679 1 chr5D.!!$R3 7678
1 TraesCS5D01G290800 chr5D 353966419 353971577 5158 True 1432.250000 2145 87.990500 2752 6588 4 chr5D.!!$R5 3836
2 TraesCS5D01G290800 chr5D 353955017 353959776 4759 True 689.000000 1129 90.833333 4560 6815 3 chr5D.!!$R4 2255
3 TraesCS5D01G290800 chr5D 388382155 388385896 3741 True 656.666667 1170 87.559000 2847 6809 6 chr5D.!!$R6 3962
4 TraesCS5D01G290800 chr5B 467021038 467026030 4992 True 1995.000000 5256 88.691333 2 6660 3 chr5B.!!$R4 6658
5 TraesCS5D01G290800 chr5B 488711277 488711800 523 True 577.000000 577 86.957000 796 1328 1 chr5B.!!$R1 532
6 TraesCS5D01G290800 chr5A 491585609 491590904 5295 True 1218.233333 4859 92.733333 2 6630 6 chr5A.!!$R4 6628
7 TraesCS5D01G290800 chr5A 113804988 113805863 875 False 1175.000000 1175 91.106000 6816 7679 1 chr5A.!!$F1 863
8 TraesCS5D01G290800 chr5A 634631425 634632320 895 True 1077.000000 1077 88.951000 6816 7679 1 chr5A.!!$R1 863
9 TraesCS5D01G290800 chr5A 552236072 552236964 892 False 1057.000000 1057 88.603000 6816 7679 1 chr5A.!!$F2 863
10 TraesCS5D01G290800 chr5A 491570129 491573595 3466 True 820.200000 2141 87.572800 2837 6815 5 chr5A.!!$R3 3978
11 TraesCS5D01G290800 chr5A 650515796 650516325 529 True 606.000000 606 87.703000 794 1328 1 chr5A.!!$R2 534
12 TraesCS5D01G290800 chr4B 31866434 31872413 5979 False 1193.750000 1495 89.839500 2683 6651 4 chr4B.!!$F2 3968
13 TraesCS5D01G290800 chr4B 356000152 356000983 831 False 953.000000 953 87.456000 4831 5667 1 chr4B.!!$F1 836
14 TraesCS5D01G290800 chr7D 525762946 525763821 875 True 1197.000000 1197 91.572000 6816 7679 1 chr7D.!!$R2 863
15 TraesCS5D01G290800 chr7D 47976977 47977596 619 True 455.000000 773 94.954000 1175 1892 2 chr7D.!!$R3 717
16 TraesCS5D01G290800 chr7D 104890665 104891328 663 False 321.000000 361 86.108000 490 2723 2 chr7D.!!$F1 2233
17 TraesCS5D01G290800 chr4D 488871831 488872707 876 True 1181.000000 1181 91.250000 6816 7679 1 chr4D.!!$R3 863
18 TraesCS5D01G290800 chr4D 315359852 315361014 1162 False 564.666667 795 95.576333 1175 2397 3 chr4D.!!$F1 1222
19 TraesCS5D01G290800 chr4D 424550008 424550889 881 True 421.333333 774 95.708667 1456 2397 3 chr4D.!!$R4 941
20 TraesCS5D01G290800 chr1B 548682306 548683177 871 False 1177.000000 1177 91.210000 6816 7679 1 chr1B.!!$F3 863
21 TraesCS5D01G290800 chr1B 539843671 539844544 873 False 1103.000000 1103 89.640000 6807 7679 1 chr1B.!!$F2 872
22 TraesCS5D01G290800 chr1B 58983881 58984402 521 True 459.000000 459 83.150000 795 1321 1 chr1B.!!$R3 526
23 TraesCS5D01G290800 chr4A 45872203 45875704 3501 True 630.166667 1153 87.652833 2970 6815 6 chr4A.!!$R4 3845
24 TraesCS5D01G290800 chr4A 702024318 702024868 550 True 623.000000 623 87.435000 774 1328 1 chr4A.!!$R3 554
25 TraesCS5D01G290800 chr6D 45802747 45803624 877 True 1149.000000 1149 90.568000 6815 7679 1 chr6D.!!$R1 864
26 TraesCS5D01G290800 chr3B 575280161 575281031 870 True 1136.000000 1136 90.422000 6816 7679 1 chr3B.!!$R2 863
27 TraesCS5D01G290800 chr3B 13522649 13523513 864 True 1072.000000 1072 89.180000 6815 7679 1 chr3B.!!$R1 864
28 TraesCS5D01G290800 chr3B 756616398 756616947 549 False 610.000000 610 87.086000 774 1328 1 chr3B.!!$F2 554
29 TraesCS5D01G290800 chr2B 80544140 80545010 870 False 1120.000000 1120 90.158000 6816 7679 1 chr2B.!!$F1 863
30 TraesCS5D01G290800 chr2B 729782933 729785950 3017 True 344.000000 573 95.063000 1175 1881 2 chr2B.!!$R2 706
31 TraesCS5D01G290800 chr7A 689943423 689944317 894 True 1094.000000 1094 89.286000 6815 7679 1 chr7A.!!$R2 864
32 TraesCS5D01G290800 chr7A 109342927 109343584 657 False 237.066667 357 90.835000 490 2723 3 chr7A.!!$F1 2233
33 TraesCS5D01G290800 chr6B 130318471 130319221 750 False 994.000000 994 90.824000 6816 7554 1 chr6B.!!$F1 738
34 TraesCS5D01G290800 chr6A 117579014 117579894 880 True 946.000000 946 86.425000 6816 7679 1 chr6A.!!$R2 863
35 TraesCS5D01G290800 chr6A 116951880 116952430 550 True 617.000000 617 87.260000 774 1328 1 chr6A.!!$R1 554
36 TraesCS5D01G290800 chr6A 143073650 143074179 529 False 606.000000 606 87.681000 795 1328 1 chr6A.!!$F1 533
37 TraesCS5D01G290800 chr3D 21407838 21411366 3528 True 744.000000 839 97.192500 1175 2397 2 chr3D.!!$R4 1222
38 TraesCS5D01G290800 chr3D 92856061 92856655 594 True 573.000000 573 84.314000 795 1395 1 chr3D.!!$R2 600
39 TraesCS5D01G290800 chr3D 592848392 592849557 1165 True 566.333333 778 95.289667 1175 2397 3 chr3D.!!$R6 1222
40 TraesCS5D01G290800 chr2D 179876875 179878039 1164 True 584.000000 822 95.972000 1175 2397 3 chr2D.!!$R2 1222
41 TraesCS5D01G290800 chr2D 603007948 603008577 629 False 450.000000 765 94.775500 1808 2397 2 chr2D.!!$F2 589
42 TraesCS5D01G290800 chr2D 473100470 473101121 651 True 349.500000 353 88.179500 502 2717 2 chr2D.!!$R3 2215
43 TraesCS5D01G290800 chr2D 62386533 62387181 648 False 222.833333 307 89.311000 503 2726 3 chr2D.!!$F1 2223
44 TraesCS5D01G290800 chr2A 631847369 631848146 777 False 507.000000 590 91.441500 791 2397 2 chr2A.!!$F1 1606

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
320 598 0.387565 GCCACTTGCCGGAAGAAAAA 59.612 50.000 5.05 0.0 35.42 1.94 F
1077 1469 0.112412 TCCTTCTCCTTTGCAACCCC 59.888 55.000 0.00 0.0 0.00 4.95 F
1794 4596 0.107703 AGCCGAATGGAGCGATGAAA 60.108 50.000 0.00 0.0 37.49 2.69 F
3345 8647 0.038166 GGTTTCTCATCCCTGGTGCA 59.962 55.000 0.00 0.0 0.00 4.57 F
4333 11750 0.320946 GTACACCCACGCTTGGCTTA 60.321 55.000 3.07 0.0 42.35 3.09 F
5128 12703 3.364366 CCAAAGCTAGCAGTCAGAAAACG 60.364 47.826 18.83 0.0 0.00 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1775 4577 0.107703 TTTCATCGCTCCATTCGGCT 60.108 50.000 0.00 0.0 0.00 5.52 R
2020 7289 1.344114 TGGCCTTGATTTTGCTCCAAC 59.656 47.619 3.32 0.0 0.00 3.77 R
3790 11169 1.229428 CGCAACCAGTGTCAACAGAT 58.771 50.000 0.00 0.0 0.00 2.90 R
4523 12042 1.694150 TCATAGCCATGCCTGTAGACC 59.306 52.381 0.00 0.0 31.73 3.85 R
5767 15842 1.071699 ACCCAACATAGTCGCAGTGTT 59.928 47.619 0.00 0.0 36.57 3.32 R
6755 17151 0.033781 GTTGTGTGGCCGTGTAGGTA 59.966 55.000 0.00 0.0 43.70 3.08 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
50 51 4.441792 CGGATGGTGATTGTGTATTCTCA 58.558 43.478 0.00 0.00 0.00 3.27
69 70 5.770919 TCTCATCAGAAGAAGGATAGGTGA 58.229 41.667 0.00 0.00 0.00 4.02
121 123 5.856986 ACTCGGTATGTGAATATCGAAATCG 59.143 40.000 3.04 0.00 38.91 3.34
159 161 4.148128 ACTGGTTGAGATCATCCATGTC 57.852 45.455 11.98 0.00 42.80 3.06
246 502 0.691078 ATTTAGCTCCTCCCCTCGCA 60.691 55.000 0.00 0.00 0.00 5.10
289 566 4.845580 CTAGGCAGCCCAGGCACG 62.846 72.222 8.22 2.43 44.88 5.34
320 598 0.387565 GCCACTTGCCGGAAGAAAAA 59.612 50.000 5.05 0.00 35.42 1.94
343 621 2.124320 ACCAGCAAACACAGCCGT 60.124 55.556 0.00 0.00 0.00 5.68
445 738 4.329545 GCCTGGTTCCGTGCCTCA 62.330 66.667 0.00 0.00 0.00 3.86
485 783 4.096003 CCCTGCCGTGTCCCGATT 62.096 66.667 0.00 0.00 39.56 3.34
589 938 5.779771 AGATTTCTGCCTGTTCCCAAATTTA 59.220 36.000 0.00 0.00 0.00 1.40
665 1023 1.372623 GCTTGCTGTGCTCCTTTGC 60.373 57.895 0.00 0.00 0.00 3.68
681 1043 7.331440 TGCTCCTTTGCAAATTGTAATGTATTG 59.669 33.333 13.23 0.00 40.29 1.90
705 1074 3.350833 ACTGAATTCTGTCCAGGAATGC 58.649 45.455 11.82 0.00 34.19 3.56
769 1139 3.285484 GAATCCATGTGGCATCTTGAGT 58.715 45.455 0.00 0.00 34.44 3.41
875 1249 1.202268 CCGAACGGAATAGCTTCTCGT 60.202 52.381 7.53 0.00 38.82 4.18
878 1252 2.778187 ACGGAATAGCTTCTCGTAGC 57.222 50.000 0.00 0.00 36.88 3.58
904 1278 1.019673 CAATCCAGGAAGCCACGATG 58.980 55.000 0.00 0.00 0.00 3.84
982 1356 2.927477 CGGAAGCTGCAGTTATTTACGA 59.073 45.455 16.64 0.00 0.00 3.43
994 1368 2.341846 ATTTACGACCGGATTGCCAT 57.658 45.000 9.46 0.00 0.00 4.40
1017 1391 1.658968 CAAGAAAAACGGTTCGCTCG 58.341 50.000 0.00 0.00 32.50 5.03
1034 1408 0.171231 TCGTCATCTCCAACTCGCTG 59.829 55.000 0.00 0.00 0.00 5.18
1046 1428 1.078848 CTCGCTGAGAAACCCCCTG 60.079 63.158 0.00 0.00 0.00 4.45
1060 1451 2.692741 CCTGTCCCCTTCCCCTCC 60.693 72.222 0.00 0.00 0.00 4.30
1077 1469 0.112412 TCCTTCTCCTTTGCAACCCC 59.888 55.000 0.00 0.00 0.00 4.95
1317 1710 2.284331 TAGGAGCGGCACCAGGAA 60.284 61.111 18.68 0.00 0.00 3.36
1339 1732 3.782443 ACGCCCCCGAAGCCTAAG 61.782 66.667 0.00 0.00 38.29 2.18
1374 1767 0.913205 GTCCCCTTCTCTTCTTCCCC 59.087 60.000 0.00 0.00 0.00 4.81
1409 1802 3.260740 CTGGCTCATGTTCTCTGTTCTC 58.739 50.000 0.00 0.00 0.00 2.87
1435 1828 6.208644 ACATGTGTGCAGTTTATTTTCAGAC 58.791 36.000 0.00 0.00 0.00 3.51
1618 4420 9.914131 ATGTACTGCTATATGTGTGTAGTTATG 57.086 33.333 0.00 0.00 0.00 1.90
1659 4461 7.477144 TGTGTGCAAATGTACTGCTATATAC 57.523 36.000 7.07 0.00 40.59 1.47
1660 4462 7.272244 TGTGTGCAAATGTACTGCTATATACT 58.728 34.615 7.07 0.00 40.59 2.12
1661 4463 8.417884 TGTGTGCAAATGTACTGCTATATACTA 58.582 33.333 7.07 0.00 40.59 1.82
1662 4464 8.916654 GTGTGCAAATGTACTGCTATATACTAG 58.083 37.037 7.07 0.00 40.59 2.57
1663 4465 8.638873 TGTGCAAATGTACTGCTATATACTAGT 58.361 33.333 0.00 0.00 40.59 2.57
1664 4466 9.477484 GTGCAAATGTACTGCTATATACTAGTT 57.523 33.333 0.00 0.00 40.59 2.24
1665 4467 9.692749 TGCAAATGTACTGCTATATACTAGTTC 57.307 33.333 0.00 0.00 40.59 3.01
1666 4468 9.692749 GCAAATGTACTGCTATATACTAGTTCA 57.307 33.333 0.00 0.00 36.84 3.18
1684 4486 9.823647 ACTAGTTCAGATATTACATGAGTTTGG 57.176 33.333 0.00 0.00 0.00 3.28
1685 4487 7.559590 AGTTCAGATATTACATGAGTTTGGC 57.440 36.000 0.00 0.00 0.00 4.52
1686 4488 7.341805 AGTTCAGATATTACATGAGTTTGGCT 58.658 34.615 0.00 0.00 0.00 4.75
1687 4489 8.486210 AGTTCAGATATTACATGAGTTTGGCTA 58.514 33.333 0.00 0.00 0.00 3.93
1689 4491 8.837788 TCAGATATTACATGAGTTTGGCTATG 57.162 34.615 0.00 0.00 0.00 2.23
1692 4494 5.762825 ATTACATGAGTTTGGCTATGCAG 57.237 39.130 0.00 0.00 0.00 4.41
1694 4496 3.689347 ACATGAGTTTGGCTATGCAGAA 58.311 40.909 0.00 0.00 0.00 3.02
1695 4497 4.081406 ACATGAGTTTGGCTATGCAGAAA 58.919 39.130 0.00 0.00 0.00 2.52
1696 4498 4.523943 ACATGAGTTTGGCTATGCAGAAAA 59.476 37.500 0.00 0.00 0.00 2.29
1700 4502 5.181245 TGAGTTTGGCTATGCAGAAAAGTAC 59.819 40.000 0.00 0.00 0.00 2.73
1702 4504 5.534654 AGTTTGGCTATGCAGAAAAGTACAA 59.465 36.000 0.00 0.00 0.00 2.41
1707 4509 7.090173 TGGCTATGCAGAAAAGTACAATTTTC 58.910 34.615 10.76 10.76 45.45 2.29
1708 4510 7.090173 GGCTATGCAGAAAAGTACAATTTTCA 58.910 34.615 17.66 8.86 46.81 2.69
1710 4512 9.787532 GCTATGCAGAAAAGTACAATTTTCATA 57.212 29.630 17.66 13.52 46.81 2.15
1732 4534 9.817809 TCATATTTGTCCTAGTACATTGAAGAC 57.182 33.333 0.00 0.00 0.00 3.01
1733 4535 9.046296 CATATTTGTCCTAGTACATTGAAGACC 57.954 37.037 0.00 0.00 0.00 3.85
1735 4537 6.428083 TTGTCCTAGTACATTGAAGACCAA 57.572 37.500 0.00 0.00 39.41 3.67
1736 4538 6.428083 TGTCCTAGTACATTGAAGACCAAA 57.572 37.500 0.00 0.00 38.43 3.28
1737 4539 6.464222 TGTCCTAGTACATTGAAGACCAAAG 58.536 40.000 0.00 0.00 38.43 2.77
1738 4540 6.042781 TGTCCTAGTACATTGAAGACCAAAGT 59.957 38.462 0.00 0.00 39.64 2.66
1739 4541 6.369065 GTCCTAGTACATTGAAGACCAAAGTG 59.631 42.308 0.00 0.00 37.29 3.16
1740 4542 6.269077 TCCTAGTACATTGAAGACCAAAGTGA 59.731 38.462 0.00 0.00 37.29 3.41
1741 4543 6.369065 CCTAGTACATTGAAGACCAAAGTGAC 59.631 42.308 0.00 0.00 37.29 3.67
1742 4544 5.680619 AGTACATTGAAGACCAAAGTGACA 58.319 37.500 0.00 0.00 37.29 3.58
1743 4545 6.299141 AGTACATTGAAGACCAAAGTGACAT 58.701 36.000 0.00 0.00 37.29 3.06
1744 4546 5.443185 ACATTGAAGACCAAAGTGACATG 57.557 39.130 0.00 0.00 35.60 3.21
1745 4547 3.988379 TTGAAGACCAAAGTGACATGC 57.012 42.857 0.00 0.00 0.00 4.06
1746 4548 2.929641 TGAAGACCAAAGTGACATGCA 58.070 42.857 0.00 0.00 0.00 3.96
1747 4549 3.489355 TGAAGACCAAAGTGACATGCAT 58.511 40.909 0.00 0.00 0.00 3.96
1748 4550 3.890756 TGAAGACCAAAGTGACATGCATT 59.109 39.130 0.00 0.00 0.00 3.56
1749 4551 4.341806 TGAAGACCAAAGTGACATGCATTT 59.658 37.500 0.00 0.00 0.00 2.32
1750 4552 4.942761 AGACCAAAGTGACATGCATTTT 57.057 36.364 0.00 0.00 36.95 1.82
1751 4553 5.280654 AGACCAAAGTGACATGCATTTTT 57.719 34.783 0.00 0.00 34.62 1.94
1774 4576 7.945033 TTTTTAGAGAAATGTCAAATGTGGC 57.055 32.000 0.00 0.00 0.00 5.01
1775 4577 6.647334 TTTAGAGAAATGTCAAATGTGGCA 57.353 33.333 0.00 0.00 45.26 4.92
1776 4578 4.778534 AGAGAAATGTCAAATGTGGCAG 57.221 40.909 0.00 0.00 44.15 4.85
1777 4579 3.057033 AGAGAAATGTCAAATGTGGCAGC 60.057 43.478 0.00 0.00 44.15 5.25
1778 4580 2.028748 AGAAATGTCAAATGTGGCAGCC 60.029 45.455 3.66 3.66 44.15 4.85
1779 4581 0.244450 AATGTCAAATGTGGCAGCCG 59.756 50.000 7.03 0.00 44.15 5.52
1780 4582 0.608856 ATGTCAAATGTGGCAGCCGA 60.609 50.000 7.03 0.00 44.15 5.54
1781 4583 0.821301 TGTCAAATGTGGCAGCCGAA 60.821 50.000 7.03 0.00 33.34 4.30
1782 4584 0.527565 GTCAAATGTGGCAGCCGAAT 59.472 50.000 7.03 0.00 0.00 3.34
1783 4585 0.527113 TCAAATGTGGCAGCCGAATG 59.473 50.000 7.03 1.55 0.00 2.67
1784 4586 0.458889 CAAATGTGGCAGCCGAATGG 60.459 55.000 7.03 0.00 38.77 3.16
1785 4587 0.611618 AAATGTGGCAGCCGAATGGA 60.612 50.000 7.03 0.00 37.49 3.41
1786 4588 1.033746 AATGTGGCAGCCGAATGGAG 61.034 55.000 7.03 0.00 37.49 3.86
1787 4589 3.512516 GTGGCAGCCGAATGGAGC 61.513 66.667 7.03 0.00 37.49 4.70
1789 4591 4.838152 GGCAGCCGAATGGAGCGA 62.838 66.667 0.00 0.00 38.34 4.93
1790 4592 2.590007 GCAGCCGAATGGAGCGAT 60.590 61.111 0.00 0.00 37.49 4.58
1791 4593 2.890109 GCAGCCGAATGGAGCGATG 61.890 63.158 0.00 0.00 37.49 3.84
1792 4594 1.227350 CAGCCGAATGGAGCGATGA 60.227 57.895 0.00 0.00 37.49 2.92
1793 4595 0.811219 CAGCCGAATGGAGCGATGAA 60.811 55.000 0.00 0.00 37.49 2.57
1794 4596 0.107703 AGCCGAATGGAGCGATGAAA 60.108 50.000 0.00 0.00 37.49 2.69
1795 4597 0.732571 GCCGAATGGAGCGATGAAAA 59.267 50.000 0.00 0.00 37.49 2.29
1796 4598 1.531883 GCCGAATGGAGCGATGAAAAC 60.532 52.381 0.00 0.00 37.49 2.43
1797 4599 1.737236 CCGAATGGAGCGATGAAAACA 59.263 47.619 0.00 0.00 37.49 2.83
1798 4600 2.476185 CCGAATGGAGCGATGAAAACAC 60.476 50.000 0.00 0.00 37.49 3.32
1799 4601 2.416547 CGAATGGAGCGATGAAAACACT 59.583 45.455 0.00 0.00 0.00 3.55
1800 4602 3.484229 CGAATGGAGCGATGAAAACACTC 60.484 47.826 0.00 0.00 0.00 3.51
1801 4603 1.428448 TGGAGCGATGAAAACACTCG 58.572 50.000 0.00 0.00 35.57 4.18
1802 4604 0.721718 GGAGCGATGAAAACACTCGG 59.278 55.000 0.00 0.00 33.17 4.63
1803 4605 1.671850 GGAGCGATGAAAACACTCGGA 60.672 52.381 0.00 0.00 33.17 4.55
1816 4618 8.500773 TGAAAACACTCGGATTGTCTTTATTAC 58.499 33.333 1.21 0.00 0.00 1.89
1823 4625 6.837992 TCGGATTGTCTTTATTACAACTTGC 58.162 36.000 0.00 0.00 39.51 4.01
1857 6258 6.542370 GGAATATTTGTGGCACTGTAGTACAT 59.458 38.462 19.83 0.00 0.00 2.29
1892 6293 4.582701 AGAACGATCTTCATCTAGGCTG 57.417 45.455 0.00 0.00 29.15 4.85
1920 7189 3.678289 TCTGCTGTTGTATGTCATGCTT 58.322 40.909 2.45 0.00 0.00 3.91
1946 7215 2.910688 ATCCGGTTCTGCATACGAAT 57.089 45.000 0.00 0.00 0.00 3.34
1959 7228 4.079028 GCATACGAATGTACGTGTTGTTG 58.921 43.478 0.00 0.00 46.02 3.33
1960 7229 4.376615 GCATACGAATGTACGTGTTGTTGT 60.377 41.667 0.00 0.00 46.02 3.32
1961 7230 5.672051 CATACGAATGTACGTGTTGTTGTT 58.328 37.500 0.00 0.00 46.02 2.83
2020 7289 4.724036 GCCACGAAAATTAAGTAGTGAGCG 60.724 45.833 7.39 0.00 0.00 5.03
2056 7325 2.165998 GGCCAAGAAACAGAGCAATCT 58.834 47.619 0.00 0.00 0.00 2.40
2060 7329 5.178797 GCCAAGAAACAGAGCAATCTACTA 58.821 41.667 0.00 0.00 0.00 1.82
2066 7335 5.667539 AACAGAGCAATCTACTAGCAGAA 57.332 39.130 0.00 0.00 0.00 3.02
2163 7433 2.665603 GCCCAGCTCGTTTCTCCT 59.334 61.111 0.00 0.00 0.00 3.69
2164 7434 1.003233 GCCCAGCTCGTTTCTCCTT 60.003 57.895 0.00 0.00 0.00 3.36
2341 7611 2.411904 GTGAAGTGAGAAGTGAGGCTG 58.588 52.381 0.00 0.00 0.00 4.85
2459 7743 8.481974 TTTGAATCAATAAATGCCATTGTCAG 57.518 30.769 0.00 0.00 35.36 3.51
2472 7756 4.380233 GCCATTGTCAGATTGAAGAACAGG 60.380 45.833 0.00 0.00 0.00 4.00
2493 7777 3.535561 GATGTCAACTAGGTCCACATGG 58.464 50.000 6.61 0.00 0.00 3.66
2506 7797 6.533730 AGGTCCACATGGTTACATATATGTG 58.466 40.000 25.48 11.90 46.06 3.21
2542 7833 5.353400 AGAATGAACACATGCACATAGTCTG 59.647 40.000 0.00 0.00 0.00 3.51
2648 7939 8.158169 TCATATTGATCAGTTTCTATTGTGCC 57.842 34.615 0.00 0.00 0.00 5.01
2736 8029 1.271926 ACTGCCGCTGGGTAATTTCTT 60.272 47.619 2.06 0.00 34.97 2.52
2768 8061 9.897744 CTCTTGAGCAGTGTATTTTTATTTTCA 57.102 29.630 0.00 0.00 0.00 2.69
2863 8156 8.952278 TGCTTTATGTACTTAATTGGATCGTTT 58.048 29.630 2.35 0.00 0.00 3.60
2894 8192 9.699410 TTGAGTTTAAATTCTACATCCATCCAT 57.301 29.630 11.47 0.00 0.00 3.41
2915 8213 3.916035 TGACCTAGACATGGCAGATACT 58.084 45.455 0.00 0.00 0.00 2.12
2920 8218 3.377346 AGACATGGCAGATACTAAGCG 57.623 47.619 0.00 0.00 0.00 4.68
3345 8647 0.038166 GGTTTCTCATCCCTGGTGCA 59.962 55.000 0.00 0.00 0.00 4.57
3448 8754 5.047802 CACATTGGCAGAAGTAATGTCCTTT 60.048 40.000 0.00 0.00 41.60 3.11
3449 8755 5.539955 ACATTGGCAGAAGTAATGTCCTTTT 59.460 36.000 0.00 0.00 40.01 2.27
3759 11138 2.828661 ATAAGAGGCTTTTGGGGGTC 57.171 50.000 0.00 0.00 0.00 4.46
3790 11169 1.310904 GTCCCAGGTGCGTTTTGTTA 58.689 50.000 0.00 0.00 0.00 2.41
3932 11335 9.807649 AATATTGAAATTTGAATCTGTGGTAGC 57.192 29.630 6.12 0.00 0.00 3.58
4245 11659 0.807496 GCAGATGGCTGAACCTGTTC 59.193 55.000 3.07 3.07 45.17 3.18
4333 11750 0.320946 GTACACCCACGCTTGGCTTA 60.321 55.000 3.07 0.00 42.35 3.09
4550 12069 4.989277 ACAGGCATGGCTATGAATGATTA 58.011 39.130 22.88 0.00 36.36 1.75
5128 12703 3.364366 CCAAAGCTAGCAGTCAGAAAACG 60.364 47.826 18.83 0.00 0.00 3.60
5429 15461 5.129485 AGTGGTAGGAAGTGATACAGAATGG 59.871 44.000 0.00 0.00 43.62 3.16
5565 15606 6.212235 AGTGACATTCTTATGCTAGATGACG 58.788 40.000 0.00 0.00 35.03 4.35
5767 15842 4.518970 GGATTGTGCTTACTGGAAGACAAA 59.481 41.667 16.25 3.35 38.02 2.83
5782 15871 3.728845 AGACAAAACACTGCGACTATGT 58.271 40.909 0.00 0.00 0.00 2.29
5784 15873 4.024893 AGACAAAACACTGCGACTATGTTG 60.025 41.667 0.00 0.00 36.69 3.33
5785 15874 3.003275 ACAAAACACTGCGACTATGTTGG 59.997 43.478 0.00 0.00 36.69 3.77
5786 15875 1.808411 AACACTGCGACTATGTTGGG 58.192 50.000 0.00 0.00 35.28 4.12
5787 15876 0.685097 ACACTGCGACTATGTTGGGT 59.315 50.000 0.00 0.00 0.00 4.51
5788 15877 1.078709 CACTGCGACTATGTTGGGTG 58.921 55.000 0.00 0.00 0.00 4.61
5789 15878 0.673644 ACTGCGACTATGTTGGGTGC 60.674 55.000 0.00 0.00 0.00 5.01
5790 15879 1.695893 CTGCGACTATGTTGGGTGCG 61.696 60.000 0.00 0.00 0.00 5.34
5791 15880 1.740296 GCGACTATGTTGGGTGCGT 60.740 57.895 0.00 0.00 0.00 5.24
5792 15881 1.966493 GCGACTATGTTGGGTGCGTG 61.966 60.000 0.00 0.00 0.00 5.34
5793 15882 0.669318 CGACTATGTTGGGTGCGTGT 60.669 55.000 0.00 0.00 0.00 4.49
5794 15883 1.519408 GACTATGTTGGGTGCGTGTT 58.481 50.000 0.00 0.00 0.00 3.32
5795 15884 1.877443 GACTATGTTGGGTGCGTGTTT 59.123 47.619 0.00 0.00 0.00 2.83
5796 15885 3.068560 GACTATGTTGGGTGCGTGTTTA 58.931 45.455 0.00 0.00 0.00 2.01
5797 15886 3.478509 ACTATGTTGGGTGCGTGTTTAA 58.521 40.909 0.00 0.00 0.00 1.52
5798 15887 4.076394 ACTATGTTGGGTGCGTGTTTAAT 58.924 39.130 0.00 0.00 0.00 1.40
5799 15888 2.783828 TGTTGGGTGCGTGTTTAATG 57.216 45.000 0.00 0.00 0.00 1.90
5800 15889 2.025155 TGTTGGGTGCGTGTTTAATGT 58.975 42.857 0.00 0.00 0.00 2.71
5801 15890 2.223595 TGTTGGGTGCGTGTTTAATGTG 60.224 45.455 0.00 0.00 0.00 3.21
5806 15895 1.784283 GTGCGTGTTTAATGTGTTGCC 59.216 47.619 0.00 0.00 0.00 4.52
5892 15983 1.297664 GTGTTGCCAAAATGCTGCAA 58.702 45.000 6.36 0.00 42.28 4.08
6135 16300 5.447010 GCTGCACTTTTGACATATCAGAGAC 60.447 44.000 0.00 0.00 35.83 3.36
6175 16340 2.203538 ACCCCAGCCAAGCAACAG 60.204 61.111 0.00 0.00 0.00 3.16
6273 16465 7.651808 CAACTACCAAATGATGAAAACACTCT 58.348 34.615 0.00 0.00 0.00 3.24
6642 17026 8.837788 TCACATGACATATCCAGATAATTGAC 57.162 34.615 0.00 0.00 0.00 3.18
6654 17038 5.360591 CAGATAATTGACGAGGTTTAGGCT 58.639 41.667 0.00 0.00 0.00 4.58
6679 17068 1.007271 CAATCGTCTCGGGCGCTAT 60.007 57.895 7.64 0.00 0.00 2.97
6691 17084 3.449377 TCGGGCGCTATGGATCATTATTA 59.551 43.478 7.64 0.00 0.00 0.98
6693 17086 4.130118 GGGCGCTATGGATCATTATTAGG 58.870 47.826 7.64 0.00 0.00 2.69
6710 17103 0.330604 AGGCCACAATCATGCACTCT 59.669 50.000 5.01 0.00 0.00 3.24
6743 17139 8.297426 TCGATCATGTACTTTCATATGGTCTAC 58.703 37.037 2.13 0.00 30.41 2.59
6755 17151 7.914427 TCATATGGTCTACATAAGAGGTGTT 57.086 36.000 2.13 0.00 44.75 3.32
6756 17152 9.429109 TTCATATGGTCTACATAAGAGGTGTTA 57.571 33.333 2.13 0.00 44.75 2.41
6758 17154 5.927281 TGGTCTACATAAGAGGTGTTACC 57.073 43.478 0.00 0.00 38.99 2.85
6759 17155 6.203072 ATGGTCTACATAAGAGGTGTTACCT 58.797 40.000 0.00 0.00 45.09 3.08
6760 17156 7.359849 ATGGTCTACATAAGAGGTGTTACCTA 58.640 38.462 0.00 0.00 43.40 3.08
6761 17157 7.287235 ATGGTCTACATAAGAGGTGTTACCTAC 59.713 40.741 0.00 0.00 43.40 3.18
6803 17199 7.934855 ACTTTCTCATTCAATCATGCTTACT 57.065 32.000 0.00 0.00 0.00 2.24
6858 17257 6.411376 ACCACATTTCACGTAATCATCCTAA 58.589 36.000 0.00 0.00 0.00 2.69
6932 17332 7.962964 TTTCGTGACAAAAACTATCAGATCT 57.037 32.000 0.00 0.00 0.00 2.75
6997 17452 3.066814 GCCTACCGGTCAGGACGT 61.067 66.667 25.44 0.00 45.00 4.34
6998 17453 2.643232 GCCTACCGGTCAGGACGTT 61.643 63.158 25.44 0.00 45.00 3.99
6999 17454 1.315257 GCCTACCGGTCAGGACGTTA 61.315 60.000 25.44 1.49 45.00 3.18
7117 17703 4.019513 TCGTCCTCCCCACCCCAT 62.020 66.667 0.00 0.00 0.00 4.00
7396 18422 4.020617 CCTTGTCCTGCTGGCGGA 62.021 66.667 4.42 2.83 0.00 5.54
7482 18511 7.858382 CACGATATATAGGCTAGTTGCATAGTC 59.142 40.741 0.00 0.00 41.42 2.59
7484 18513 8.406297 CGATATATAGGCTAGTTGCATAGTCAA 58.594 37.037 0.00 0.00 41.42 3.18
7620 18848 8.560355 ACTGTCATACACTAAATATTGTGCAA 57.440 30.769 5.97 0.00 37.68 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 2.192175 GGCCCCCATTCCACTACG 59.808 66.667 0.00 0.00 0.00 3.51
50 51 5.222870 ACCATCACCTATCCTTCTTCTGAT 58.777 41.667 0.00 0.00 0.00 2.90
69 70 0.033208 CCCACTGCCCACAATACCAT 60.033 55.000 0.00 0.00 0.00 3.55
121 123 2.608752 CCAGTTCCACTTCAATGCAAGC 60.609 50.000 0.00 0.00 0.00 4.01
159 161 2.355513 CCCTCTCATTTCCCACACTCAG 60.356 54.545 0.00 0.00 0.00 3.35
221 275 4.228010 GAGGGGAGGAGCTAAATTAGTCT 58.772 47.826 1.68 0.00 0.00 3.24
320 598 2.345876 GCTGTGTTTGCTGGTGTTTTT 58.654 42.857 0.00 0.00 0.00 1.94
325 603 2.332514 CGGCTGTGTTTGCTGGTG 59.667 61.111 0.00 0.00 33.50 4.17
326 604 2.124320 ACGGCTGTGTTTGCTGGT 60.124 55.556 0.00 0.00 40.81 4.00
373 651 3.050275 GAACGGGAGGCAGTGCAC 61.050 66.667 18.61 9.40 0.00 4.57
374 652 4.329545 GGAACGGGAGGCAGTGCA 62.330 66.667 18.61 0.00 0.00 4.57
427 720 4.329545 GAGGCACGGAACCAGGCA 62.330 66.667 8.87 0.00 0.00 4.75
445 738 1.211190 GGCGAGTAAAGTCGACGGT 59.789 57.895 10.46 4.51 42.85 4.83
475 773 2.499685 CGAGGGGAATCGGGACAC 59.500 66.667 0.00 0.00 39.04 3.67
482 780 2.107141 CGACTGCCGAGGGGAATC 59.893 66.667 0.00 0.00 41.76 2.52
483 781 2.363795 TCGACTGCCGAGGGGAAT 60.364 61.111 0.00 0.00 43.23 3.01
589 938 3.367932 CACGACGAGTAATGAGCAAACAT 59.632 43.478 0.00 0.00 0.00 2.71
681 1043 3.895232 TCCTGGACAGAATTCAGTAGC 57.105 47.619 8.44 0.00 0.00 3.58
793 1166 3.454082 AGGAGATCAGAACAGGCCTTAAG 59.546 47.826 0.00 0.00 0.00 1.85
797 1170 1.494960 GAGGAGATCAGAACAGGCCT 58.505 55.000 0.00 0.00 0.00 5.19
875 1249 1.225426 CCTGGATTGCAGGCAGCTA 59.775 57.895 11.59 0.00 45.94 3.32
878 1252 1.664321 GCTTCCTGGATTGCAGGCAG 61.664 60.000 18.72 18.03 39.60 4.85
879 1253 1.679977 GCTTCCTGGATTGCAGGCA 60.680 57.895 18.72 7.87 39.60 4.75
880 1254 2.421399 GGCTTCCTGGATTGCAGGC 61.421 63.158 18.72 12.61 39.60 4.85
881 1255 1.000521 TGGCTTCCTGGATTGCAGG 60.001 57.895 17.56 17.56 41.08 4.85
982 1356 3.636929 TTGGCGATGGCAATCCGGT 62.637 57.895 0.00 0.00 42.98 5.28
994 1368 0.305313 CGAACCGTTTTTCTTGGCGA 59.695 50.000 0.00 0.00 0.00 5.54
1017 1391 1.474478 TCTCAGCGAGTTGGAGATGAC 59.526 52.381 5.66 0.00 33.01 3.06
1034 1408 1.140772 AAGGGGACAGGGGGTTTCTC 61.141 60.000 0.00 0.00 0.00 2.87
1046 1428 0.983905 GAGAAGGAGGGGAAGGGGAC 60.984 65.000 0.00 0.00 0.00 4.46
1060 1451 1.251251 CTGGGGTTGCAAAGGAGAAG 58.749 55.000 0.00 0.00 0.00 2.85
1299 1692 2.579684 CTTCCTGGTGCCGCTCCTAC 62.580 65.000 12.54 0.00 0.00 3.18
1339 1732 2.358003 ACGAGCTCACCTTGCAGC 60.358 61.111 15.40 0.00 35.73 5.25
1374 1767 1.524621 GCCAGGACACCGATCCATG 60.525 63.158 0.00 0.00 41.73 3.66
1409 1802 7.535258 GTCTGAAAATAAACTGCACACATGTAG 59.465 37.037 0.00 0.00 43.70 2.74
1435 1828 5.186996 AGGATTTTGCACACAACAAGTAG 57.813 39.130 0.00 0.00 34.87 2.57
1617 4419 5.451381 GCACACATATACCACTAGCAGTACA 60.451 44.000 0.00 0.00 0.00 2.90
1618 4420 4.982916 GCACACATATACCACTAGCAGTAC 59.017 45.833 0.00 0.00 0.00 2.73
1659 4461 8.768955 GCCAAACTCATGTAATATCTGAACTAG 58.231 37.037 0.00 0.00 0.00 2.57
1660 4462 8.486210 AGCCAAACTCATGTAATATCTGAACTA 58.514 33.333 0.00 0.00 0.00 2.24
1661 4463 7.341805 AGCCAAACTCATGTAATATCTGAACT 58.658 34.615 0.00 0.00 0.00 3.01
1662 4464 7.559590 AGCCAAACTCATGTAATATCTGAAC 57.440 36.000 0.00 0.00 0.00 3.18
1663 4465 9.276590 CATAGCCAAACTCATGTAATATCTGAA 57.723 33.333 0.00 0.00 0.00 3.02
1664 4466 7.388776 GCATAGCCAAACTCATGTAATATCTGA 59.611 37.037 0.00 0.00 0.00 3.27
1665 4467 7.173735 TGCATAGCCAAACTCATGTAATATCTG 59.826 37.037 0.00 0.00 0.00 2.90
1666 4468 7.226441 TGCATAGCCAAACTCATGTAATATCT 58.774 34.615 0.00 0.00 0.00 1.98
1667 4469 7.388776 TCTGCATAGCCAAACTCATGTAATATC 59.611 37.037 0.00 0.00 0.00 1.63
1668 4470 7.226441 TCTGCATAGCCAAACTCATGTAATAT 58.774 34.615 0.00 0.00 0.00 1.28
1669 4471 6.591001 TCTGCATAGCCAAACTCATGTAATA 58.409 36.000 0.00 0.00 0.00 0.98
1670 4472 5.439721 TCTGCATAGCCAAACTCATGTAAT 58.560 37.500 0.00 0.00 0.00 1.89
1671 4473 4.842574 TCTGCATAGCCAAACTCATGTAA 58.157 39.130 0.00 0.00 0.00 2.41
1672 4474 4.486125 TCTGCATAGCCAAACTCATGTA 57.514 40.909 0.00 0.00 0.00 2.29
1673 4475 3.354948 TCTGCATAGCCAAACTCATGT 57.645 42.857 0.00 0.00 0.00 3.21
1674 4476 4.707030 TTTCTGCATAGCCAAACTCATG 57.293 40.909 0.00 0.00 0.00 3.07
1675 4477 4.768968 ACTTTTCTGCATAGCCAAACTCAT 59.231 37.500 0.00 0.00 0.00 2.90
1676 4478 4.144297 ACTTTTCTGCATAGCCAAACTCA 58.856 39.130 0.00 0.00 0.00 3.41
1677 4479 4.773323 ACTTTTCTGCATAGCCAAACTC 57.227 40.909 0.00 0.00 0.00 3.01
1678 4480 5.070001 TGTACTTTTCTGCATAGCCAAACT 58.930 37.500 0.00 0.00 0.00 2.66
1679 4481 5.371115 TGTACTTTTCTGCATAGCCAAAC 57.629 39.130 0.00 0.00 0.00 2.93
1680 4482 6.588719 ATTGTACTTTTCTGCATAGCCAAA 57.411 33.333 0.00 0.00 0.00 3.28
1681 4483 6.588719 AATTGTACTTTTCTGCATAGCCAA 57.411 33.333 0.00 0.00 0.00 4.52
1682 4484 6.588719 AAATTGTACTTTTCTGCATAGCCA 57.411 33.333 0.00 0.00 0.00 4.75
1683 4485 7.090173 TGAAAATTGTACTTTTCTGCATAGCC 58.910 34.615 16.72 0.00 42.80 3.93
1684 4486 8.693542 ATGAAAATTGTACTTTTCTGCATAGC 57.306 30.769 16.72 0.00 42.80 2.97
1707 4509 9.046296 GGTCTTCAATGTACTAGGACAAATATG 57.954 37.037 12.92 9.26 31.83 1.78
1708 4510 8.768397 TGGTCTTCAATGTACTAGGACAAATAT 58.232 33.333 12.92 0.00 31.83 1.28
1710 4512 7.016153 TGGTCTTCAATGTACTAGGACAAAT 57.984 36.000 12.92 0.93 31.83 2.32
1715 4517 6.269077 TCACTTTGGTCTTCAATGTACTAGGA 59.731 38.462 0.00 0.00 40.39 2.94
1717 4519 6.929049 TGTCACTTTGGTCTTCAATGTACTAG 59.071 38.462 0.00 0.00 40.39 2.57
1720 4522 6.373779 CATGTCACTTTGGTCTTCAATGTAC 58.626 40.000 0.00 0.00 40.39 2.90
1721 4523 5.048782 GCATGTCACTTTGGTCTTCAATGTA 60.049 40.000 0.00 0.00 40.39 2.29
1725 4527 3.286353 TGCATGTCACTTTGGTCTTCAA 58.714 40.909 0.00 0.00 0.00 2.69
1726 4528 2.929641 TGCATGTCACTTTGGTCTTCA 58.070 42.857 0.00 0.00 0.00 3.02
1727 4529 4.510038 AATGCATGTCACTTTGGTCTTC 57.490 40.909 0.00 0.00 0.00 2.87
1728 4530 4.942761 AAATGCATGTCACTTTGGTCTT 57.057 36.364 0.00 0.00 0.00 3.01
1729 4531 4.942761 AAAATGCATGTCACTTTGGTCT 57.057 36.364 0.00 0.00 0.00 3.85
1750 4552 7.495901 TGCCACATTTGACATTTCTCTAAAAA 58.504 30.769 0.00 0.00 0.00 1.94
1751 4553 7.048629 TGCCACATTTGACATTTCTCTAAAA 57.951 32.000 0.00 0.00 0.00 1.52
1752 4554 6.647334 TGCCACATTTGACATTTCTCTAAA 57.353 33.333 0.00 0.00 0.00 1.85
1753 4555 5.335897 GCTGCCACATTTGACATTTCTCTAA 60.336 40.000 0.00 0.00 0.00 2.10
1754 4556 4.156556 GCTGCCACATTTGACATTTCTCTA 59.843 41.667 0.00 0.00 0.00 2.43
1755 4557 3.057033 GCTGCCACATTTGACATTTCTCT 60.057 43.478 0.00 0.00 0.00 3.10
1756 4558 3.248266 GCTGCCACATTTGACATTTCTC 58.752 45.455 0.00 0.00 0.00 2.87
1757 4559 2.028748 GGCTGCCACATTTGACATTTCT 60.029 45.455 15.17 0.00 0.00 2.52
1758 4560 2.340337 GGCTGCCACATTTGACATTTC 58.660 47.619 15.17 0.00 0.00 2.17
1759 4561 1.337074 CGGCTGCCACATTTGACATTT 60.337 47.619 20.29 0.00 0.00 2.32
1760 4562 0.244450 CGGCTGCCACATTTGACATT 59.756 50.000 20.29 0.00 0.00 2.71
1761 4563 0.608856 TCGGCTGCCACATTTGACAT 60.609 50.000 20.29 0.00 0.00 3.06
1762 4564 0.821301 TTCGGCTGCCACATTTGACA 60.821 50.000 20.29 0.00 0.00 3.58
1763 4565 0.527565 ATTCGGCTGCCACATTTGAC 59.472 50.000 20.29 0.00 0.00 3.18
1764 4566 0.527113 CATTCGGCTGCCACATTTGA 59.473 50.000 20.29 3.35 0.00 2.69
1765 4567 0.458889 CCATTCGGCTGCCACATTTG 60.459 55.000 20.29 8.14 0.00 2.32
1766 4568 0.611618 TCCATTCGGCTGCCACATTT 60.612 50.000 20.29 0.00 0.00 2.32
1767 4569 1.001020 TCCATTCGGCTGCCACATT 60.001 52.632 20.29 0.00 0.00 2.71
1768 4570 1.452651 CTCCATTCGGCTGCCACAT 60.453 57.895 20.29 6.63 0.00 3.21
1769 4571 2.046023 CTCCATTCGGCTGCCACA 60.046 61.111 20.29 4.14 0.00 4.17
1770 4572 3.512516 GCTCCATTCGGCTGCCAC 61.513 66.667 20.29 0.00 0.00 5.01
1772 4574 4.838152 TCGCTCCATTCGGCTGCC 62.838 66.667 9.11 9.11 0.00 4.85
1773 4575 2.590007 ATCGCTCCATTCGGCTGC 60.590 61.111 0.00 0.00 0.00 5.25
1774 4576 0.811219 TTCATCGCTCCATTCGGCTG 60.811 55.000 0.00 0.00 0.00 4.85
1775 4577 0.107703 TTTCATCGCTCCATTCGGCT 60.108 50.000 0.00 0.00 0.00 5.52
1776 4578 0.732571 TTTTCATCGCTCCATTCGGC 59.267 50.000 0.00 0.00 0.00 5.54
1777 4579 1.737236 TGTTTTCATCGCTCCATTCGG 59.263 47.619 0.00 0.00 0.00 4.30
1778 4580 2.416547 AGTGTTTTCATCGCTCCATTCG 59.583 45.455 0.00 0.00 0.00 3.34
1779 4581 3.484229 CGAGTGTTTTCATCGCTCCATTC 60.484 47.826 0.00 0.00 38.67 2.67
1780 4582 2.416547 CGAGTGTTTTCATCGCTCCATT 59.583 45.455 0.00 0.00 38.67 3.16
1781 4583 2.002586 CGAGTGTTTTCATCGCTCCAT 58.997 47.619 0.00 0.00 38.67 3.41
1782 4584 1.428448 CGAGTGTTTTCATCGCTCCA 58.572 50.000 0.00 0.00 38.67 3.86
1783 4585 0.721718 CCGAGTGTTTTCATCGCTCC 59.278 55.000 0.00 0.00 38.67 4.70
1784 4586 1.710013 TCCGAGTGTTTTCATCGCTC 58.290 50.000 0.00 0.00 38.56 5.03
1785 4587 2.386661 ATCCGAGTGTTTTCATCGCT 57.613 45.000 0.00 0.00 35.18 4.93
1786 4588 2.159627 ACAATCCGAGTGTTTTCATCGC 59.840 45.455 0.00 0.00 35.18 4.58
1787 4589 3.679980 AGACAATCCGAGTGTTTTCATCG 59.320 43.478 2.51 0.00 36.24 3.84
1788 4590 5.613358 AAGACAATCCGAGTGTTTTCATC 57.387 39.130 2.51 0.00 0.00 2.92
1789 4591 7.687941 ATAAAGACAATCCGAGTGTTTTCAT 57.312 32.000 2.51 0.00 34.74 2.57
1790 4592 7.504924 AATAAAGACAATCCGAGTGTTTTCA 57.495 32.000 2.51 0.00 34.74 2.69
1791 4593 8.500773 TGTAATAAAGACAATCCGAGTGTTTTC 58.499 33.333 2.51 0.00 34.74 2.29
1792 4594 8.385898 TGTAATAAAGACAATCCGAGTGTTTT 57.614 30.769 2.51 0.78 34.74 2.43
1793 4595 7.972832 TGTAATAAAGACAATCCGAGTGTTT 57.027 32.000 2.51 0.00 36.57 2.83
1794 4596 7.660208 AGTTGTAATAAAGACAATCCGAGTGTT 59.340 33.333 2.51 0.00 38.94 3.32
1795 4597 7.159372 AGTTGTAATAAAGACAATCCGAGTGT 58.841 34.615 0.06 0.06 38.94 3.55
1796 4598 7.596749 AGTTGTAATAAAGACAATCCGAGTG 57.403 36.000 0.00 0.00 38.94 3.51
1797 4599 7.360946 GCAAGTTGTAATAAAGACAATCCGAGT 60.361 37.037 4.48 0.00 38.94 4.18
1798 4600 6.961554 GCAAGTTGTAATAAAGACAATCCGAG 59.038 38.462 4.48 0.00 38.94 4.63
1799 4601 6.128117 GGCAAGTTGTAATAAAGACAATCCGA 60.128 38.462 4.48 0.00 38.94 4.55
1800 4602 6.027749 GGCAAGTTGTAATAAAGACAATCCG 58.972 40.000 4.48 0.00 38.94 4.18
1801 4603 7.158099 AGGCAAGTTGTAATAAAGACAATCC 57.842 36.000 4.48 0.00 38.94 3.01
1803 4605 9.908152 GTTAAGGCAAGTTGTAATAAAGACAAT 57.092 29.630 4.48 0.00 38.94 2.71
1816 4618 6.530019 AATATTCCCAGTTAAGGCAAGTTG 57.470 37.500 0.00 0.00 0.00 3.16
1823 4625 4.709397 TGCCACAAATATTCCCAGTTAAGG 59.291 41.667 0.00 0.00 0.00 2.69
1892 6293 3.412386 ACATACAACAGCAGAGGTTTCC 58.588 45.455 0.00 0.00 0.00 3.13
1920 7189 3.627395 ATGCAGAACCGGATAGTTTCA 57.373 42.857 9.46 0.00 0.00 2.69
1946 7215 2.284684 CGGCTAAACAACAACACGTACA 59.715 45.455 0.00 0.00 0.00 2.90
1973 7242 4.805192 TCGTTGTACAATTAATCTACGGCC 59.195 41.667 12.26 0.00 32.25 6.13
2020 7289 1.344114 TGGCCTTGATTTTGCTCCAAC 59.656 47.619 3.32 0.00 0.00 3.77
2056 7325 7.041030 GCTGTACATAGATCTGTTCTGCTAGTA 60.041 40.741 5.18 0.00 37.92 1.82
2060 7329 4.202202 GGCTGTACATAGATCTGTTCTGCT 60.202 45.833 5.18 0.00 39.56 4.24
2066 7335 6.258727 CGAATTTTGGCTGTACATAGATCTGT 59.741 38.462 5.18 0.00 0.00 3.41
2116 7385 1.673168 GAGTGAATGCCTGGGCTTAG 58.327 55.000 13.05 0.00 42.51 2.18
2341 7611 6.375455 TCAAAAACTTCTCATATCCAGCTTCC 59.625 38.462 0.00 0.00 0.00 3.46
2450 7734 5.005740 TCCTGTTCTTCAATCTGACAATGG 58.994 41.667 0.00 0.00 0.00 3.16
2459 7743 6.314896 CCTAGTTGACATCCTGTTCTTCAATC 59.685 42.308 0.00 0.00 0.00 2.67
2472 7756 3.055094 ACCATGTGGACCTAGTTGACATC 60.055 47.826 5.96 0.00 38.94 3.06
2493 7777 9.935682 CTTCCACATTTGACACATATATGTAAC 57.064 33.333 17.86 14.34 39.39 2.50
2506 7797 5.830912 TGTGTTCATTCTTCCACATTTGAC 58.169 37.500 0.00 0.00 33.19 3.18
2648 7939 9.537192 AATAACAAGAAATATGACATGCCAATG 57.463 29.630 0.00 0.00 39.89 2.82
2693 7986 3.002348 GGCGGATCTAGGATTTTGAAACG 59.998 47.826 0.00 0.00 0.00 3.60
2851 8144 6.515272 AACTCAATGCTAAACGATCCAATT 57.485 33.333 0.00 0.00 0.00 2.32
2863 8156 9.679661 TGGATGTAGAATTTAAACTCAATGCTA 57.320 29.630 0.00 0.00 0.00 3.49
2894 8192 3.916035 AGTATCTGCCATGTCTAGGTCA 58.084 45.455 0.00 0.00 0.00 4.02
3294 8596 3.697045 TGTTCGGAACAAGAATGGTGTTT 59.303 39.130 20.52 0.00 39.29 2.83
3345 8647 2.028876 GTTTTACAGGGGTGTGCAACT 58.971 47.619 0.00 0.00 38.04 3.16
3353 8655 5.205056 TGACAAAGATTGTTTTACAGGGGT 58.795 37.500 0.00 0.00 45.52 4.95
3448 8754 5.389520 TGTCCCAACATGAAGGATTTGTAA 58.610 37.500 0.00 0.00 30.92 2.41
3449 8755 4.991776 TGTCCCAACATGAAGGATTTGTA 58.008 39.130 0.00 0.00 30.92 2.41
3790 11169 1.229428 CGCAACCAGTGTCAACAGAT 58.771 50.000 0.00 0.00 0.00 2.90
3932 11335 0.395312 AACCGGGCGATATTGGTAGG 59.605 55.000 6.32 0.00 33.45 3.18
4053 11467 4.743644 GGTAACGAGCTTCATGTACCATAC 59.256 45.833 0.00 0.00 0.00 2.39
4245 11659 2.114616 AGGATACACTGCTCCCTTCAG 58.885 52.381 0.00 0.00 41.41 3.02
4333 11750 3.958147 AGATTTGTTTCCTTTTCGGTGGT 59.042 39.130 0.00 0.00 0.00 4.16
4372 11891 4.037222 TGGATAGGTAGCAATCAACTCCA 58.963 43.478 0.00 0.00 0.00 3.86
4523 12042 1.694150 TCATAGCCATGCCTGTAGACC 59.306 52.381 0.00 0.00 31.73 3.85
4571 12091 4.675146 GCTGCATAAATATATGGGCGGTTG 60.675 45.833 0.00 0.00 39.49 3.77
4663 12213 7.181569 TCCAAGTTGACATTTCTTCCTTTTT 57.818 32.000 3.87 0.00 0.00 1.94
4810 12380 4.318831 GCCTGCTTTTTATCCGTAAGATCG 60.319 45.833 0.00 0.00 43.02 3.69
5128 12703 3.122297 CGACTTCAGATCCTCATCTTGC 58.878 50.000 0.00 0.00 37.25 4.01
5429 15461 7.984050 TCAAGACTCTTCATCTTCATTCATACC 59.016 37.037 0.00 0.00 34.08 2.73
5530 15571 9.319143 GCATAAGAATGTCACTTCTTACTACAT 57.681 33.333 14.44 0.00 45.59 2.29
5532 15573 8.934507 AGCATAAGAATGTCACTTCTTACTAC 57.065 34.615 14.44 9.84 45.59 2.73
5535 15576 9.757227 ATCTAGCATAAGAATGTCACTTCTTAC 57.243 33.333 14.44 7.67 45.59 2.34
5537 15578 8.481314 TCATCTAGCATAAGAATGTCACTTCTT 58.519 33.333 12.12 12.12 45.18 2.52
5538 15579 7.925483 GTCATCTAGCATAAGAATGTCACTTCT 59.075 37.037 0.00 0.00 37.06 2.85
5539 15580 7.096271 CGTCATCTAGCATAAGAATGTCACTTC 60.096 40.741 0.00 0.00 35.38 3.01
5540 15581 6.699204 CGTCATCTAGCATAAGAATGTCACTT 59.301 38.462 0.00 0.00 35.38 3.16
5541 15582 6.183360 ACGTCATCTAGCATAAGAATGTCACT 60.183 38.462 0.00 0.00 35.38 3.41
5542 15583 5.980116 ACGTCATCTAGCATAAGAATGTCAC 59.020 40.000 0.00 0.00 35.38 3.67
5543 15584 6.149129 ACGTCATCTAGCATAAGAATGTCA 57.851 37.500 0.00 0.00 35.38 3.58
5544 15585 7.222805 TCAAACGTCATCTAGCATAAGAATGTC 59.777 37.037 0.00 0.00 35.38 3.06
5545 15586 7.010552 GTCAAACGTCATCTAGCATAAGAATGT 59.989 37.037 0.00 0.00 35.38 2.71
5546 15587 7.010460 TGTCAAACGTCATCTAGCATAAGAATG 59.990 37.037 0.00 0.00 36.09 2.67
5547 15588 7.041721 TGTCAAACGTCATCTAGCATAAGAAT 58.958 34.615 0.00 0.00 0.00 2.40
5548 15589 6.394809 TGTCAAACGTCATCTAGCATAAGAA 58.605 36.000 0.00 0.00 0.00 2.52
5565 15606 6.414987 GCATACTCTTGAGTGTTTTGTCAAAC 59.585 38.462 12.99 0.00 42.49 2.93
5767 15842 1.071699 ACCCAACATAGTCGCAGTGTT 59.928 47.619 0.00 0.00 36.57 3.32
5782 15871 2.025155 ACACATTAAACACGCACCCAA 58.975 42.857 0.00 0.00 0.00 4.12
5784 15873 2.389998 CAACACATTAAACACGCACCC 58.610 47.619 0.00 0.00 0.00 4.61
5785 15874 1.784283 GCAACACATTAAACACGCACC 59.216 47.619 0.00 0.00 0.00 5.01
5786 15875 1.784283 GGCAACACATTAAACACGCAC 59.216 47.619 0.00 0.00 0.00 5.34
5787 15876 1.405463 TGGCAACACATTAAACACGCA 59.595 42.857 0.00 0.00 46.17 5.24
5788 15877 2.126914 TGGCAACACATTAAACACGC 57.873 45.000 0.00 0.00 46.17 5.34
5801 15890 6.439675 AATTGCAATGGAAATAATGGCAAC 57.560 33.333 13.82 0.00 44.61 4.17
6135 16300 1.533625 TGCTCCATCAAGGTTTTCCG 58.466 50.000 0.00 0.00 46.35 4.30
6175 16340 1.375098 GGTCAGCCAGAGAAGCATGC 61.375 60.000 10.51 10.51 34.09 4.06
6273 16465 1.221466 CGTGCCAAGAAGAGAACGCA 61.221 55.000 0.00 0.00 0.00 5.24
6654 17038 1.470979 GCCCGAGACGATTGCTTCTTA 60.471 52.381 0.00 0.00 0.00 2.10
6664 17048 3.592814 CCATAGCGCCCGAGACGA 61.593 66.667 2.29 0.00 0.00 4.20
6679 17068 5.951204 TGATTGTGGCCTAATAATGATCCA 58.049 37.500 3.32 0.00 0.00 3.41
6691 17084 0.330604 AGAGTGCATGATTGTGGCCT 59.669 50.000 3.32 0.00 0.00 5.19
6693 17086 1.171308 ACAGAGTGCATGATTGTGGC 58.829 50.000 0.00 0.00 0.00 5.01
6755 17151 0.033781 GTTGTGTGGCCGTGTAGGTA 59.966 55.000 0.00 0.00 43.70 3.08
6756 17152 1.227734 GTTGTGTGGCCGTGTAGGT 60.228 57.895 0.00 0.00 43.70 3.08
6758 17154 1.227704 TGGTTGTGTGGCCGTGTAG 60.228 57.895 0.00 0.00 0.00 2.74
6759 17155 1.524165 GTGGTTGTGTGGCCGTGTA 60.524 57.895 0.00 0.00 0.00 2.90
6760 17156 2.826738 GTGGTTGTGTGGCCGTGT 60.827 61.111 0.00 0.00 0.00 4.49
6761 17157 2.410687 TTGTGGTTGTGTGGCCGTG 61.411 57.895 0.00 0.00 0.00 4.94
6762 17158 2.044848 TTGTGGTTGTGTGGCCGT 60.045 55.556 0.00 0.00 0.00 5.68
6763 17159 1.662438 AAGTTGTGGTTGTGTGGCCG 61.662 55.000 0.00 0.00 0.00 6.13
6803 17199 3.096852 TCAATTACTCCAGAGAAGGCGA 58.903 45.455 0.70 0.00 0.00 5.54
6932 17332 3.186909 CGCTTCAATCGGTCATCAACTA 58.813 45.455 0.00 0.00 0.00 2.24
7095 17681 2.675772 GTGGGGAGGACGACGAGT 60.676 66.667 0.00 0.00 0.00 4.18
7117 17703 1.984570 CAGTGAGCTCGGGGGAGAA 60.985 63.158 9.64 0.00 0.00 2.87
7177 18015 3.262686 GATTCGGCGCCGGAGTTC 61.263 66.667 44.95 30.24 40.25 3.01
7372 18398 0.615331 CAGCAGGACAAGGAAGCCTA 59.385 55.000 0.00 0.00 31.13 3.93
7374 18400 1.676967 CCAGCAGGACAAGGAAGCC 60.677 63.158 0.00 0.00 36.89 4.35
7396 18422 0.833287 ATCTGTTGCCATACCTCGCT 59.167 50.000 0.00 0.00 0.00 4.93
7484 18513 9.979578 TGCTCAAACATTGTTCTAATGTAAATT 57.020 25.926 1.83 0.00 39.73 1.82
7499 18528 4.895668 ATTCCCATTGTGCTCAAACATT 57.104 36.364 5.15 0.00 37.11 2.71


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

AutoCloner maintained by Alex Coulton.