Multiple sequence alignment - TraesCS2B01G225100

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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 TraesCS2B01G225100 chr2B 100.000 8231 0 0 1 8231 214821422 214829652 0.000000e+00 15200.0
1 TraesCS2B01G225100 chr2B 93.814 1649 75 15 3313 4934 195064932 195063284 0.000000e+00 2455.0
2 TraesCS2B01G225100 chr2B 90.335 269 23 3 4624 4891 760624053 760623787 4.730000e-92 350.0
3 TraesCS2B01G225100 chr2B 94.737 95 5 0 6704 6798 440223779 440223873 1.850000e-31 148.0
4 TraesCS2B01G225100 chr2B 89.167 120 7 6 6675 6789 715928136 715928018 2.390000e-30 145.0
5 TraesCS2B01G225100 chr2A 93.598 2749 120 28 585 3313 167332008 167334720 0.000000e+00 4050.0
6 TraesCS2B01G225100 chr2A 90.384 1799 123 17 4934 6698 167334714 167336496 0.000000e+00 2318.0
7 TraesCS2B01G225100 chr2A 89.235 771 40 21 6805 7540 167336518 167337280 0.000000e+00 924.0
8 TraesCS2B01G225100 chr2A 81.283 561 45 25 7618 8140 167337277 167337815 4.630000e-107 399.0
9 TraesCS2B01G225100 chr2A 92.523 107 3 1 6688 6789 43144665 43144559 1.850000e-31 148.0
10 TraesCS2B01G225100 chr2D 94.967 2404 87 20 3 2384 157379888 157382279 0.000000e+00 3738.0
11 TraesCS2B01G225100 chr2D 95.798 1785 52 6 4934 6698 157383225 157385006 0.000000e+00 2859.0
12 TraesCS2B01G225100 chr2D 92.484 958 21 11 2377 3313 157382304 157383231 0.000000e+00 1323.0
13 TraesCS2B01G225100 chr2D 92.798 722 38 7 6787 7495 157385005 157385725 0.000000e+00 1033.0
14 TraesCS2B01G225100 chr2D 83.829 538 55 16 2771 3306 621825285 621825792 4.470000e-132 483.0
15 TraesCS2B01G225100 chr2D 82.752 545 54 22 7618 8139 157386119 157386646 4.530000e-122 449.0
16 TraesCS2B01G225100 chr2D 86.510 341 36 3 2204 2534 621824895 621825235 4.690000e-97 366.0
17 TraesCS2B01G225100 chr2D 98.765 81 1 0 7540 7620 534925545 534925465 2.390000e-30 145.0
18 TraesCS2B01G225100 chr2D 95.506 89 4 0 7540 7628 128890719 128890631 8.610000e-30 143.0
19 TraesCS2B01G225100 chr2D 82.249 169 22 6 1960 2128 621824657 621824817 1.110000e-28 139.0
20 TraesCS2B01G225100 chr2D 92.784 97 3 3 7530 7624 262614714 262614620 4.010000e-28 137.0
21 TraesCS2B01G225100 chr1B 95.073 1644 59 2 3313 4935 316257771 316259413 0.000000e+00 2567.0
22 TraesCS2B01G225100 chr1B 93.742 1646 82 2 3311 4935 421431071 421432716 0.000000e+00 2449.0
23 TraesCS2B01G225100 chr1B 92.456 676 45 6 4260 4934 327833729 327834399 0.000000e+00 961.0
24 TraesCS2B01G225100 chr1B 92.308 676 46 6 4260 4934 327835134 327835804 0.000000e+00 955.0
25 TraesCS2B01G225100 chr1B 98.837 86 1 0 6704 6789 160464617 160464702 3.980000e-33 154.0
26 TraesCS2B01G225100 chr1B 94.505 91 4 1 7540 7630 151463479 151463390 1.110000e-28 139.0
27 TraesCS2B01G225100 chr6B 94.830 1644 55 8 3312 4934 113652051 113650417 0.000000e+00 2538.0
28 TraesCS2B01G225100 chr6B 90.341 1377 124 6 3324 4694 117703668 117702295 0.000000e+00 1797.0
29 TraesCS2B01G225100 chr6B 97.476 1030 25 1 3312 4341 124083517 124082489 0.000000e+00 1757.0
30 TraesCS2B01G225100 chr6B 97.175 531 15 0 4405 4935 124081868 124081338 0.000000e+00 898.0
31 TraesCS2B01G225100 chr6B 85.311 531 45 18 2777 3306 713798151 713798649 1.220000e-142 518.0
32 TraesCS2B01G225100 chr6B 82.593 540 47 20 2123 2649 713797633 713798138 4.560000e-117 433.0
33 TraesCS2B01G225100 chr6B 84.181 177 19 7 1960 2135 713797450 713797618 6.610000e-36 163.0
34 TraesCS2B01G225100 chr6B 97.647 85 2 0 7540 7624 13827606 13827522 6.660000e-31 147.0
35 TraesCS2B01G225100 chr6B 95.506 89 3 1 7540 7628 472612141 472612054 3.100000e-29 141.0
36 TraesCS2B01G225100 chr6B 92.857 98 4 3 7540 7635 485061282 485061186 1.110000e-28 139.0
37 TraesCS2B01G225100 chr5B 91.758 1638 118 5 3312 4933 636986999 636988635 0.000000e+00 2261.0
38 TraesCS2B01G225100 chr5B 91.105 371 30 2 2783 3153 545003357 545002990 4.440000e-137 499.0
39 TraesCS2B01G225100 chr5B 83.395 542 51 16 2123 2649 545003893 545003376 4.500000e-127 466.0
40 TraesCS2B01G225100 chr5B 84.746 177 18 6 1960 2135 545004076 545003908 1.420000e-37 169.0
41 TraesCS2B01G225100 chr5B 97.727 88 2 0 6704 6791 223038328 223038241 1.430000e-32 152.0
42 TraesCS2B01G225100 chr5B 94.505 91 4 1 7540 7630 264876382 264876293 1.110000e-28 139.0
43 TraesCS2B01G225100 chr3B 95.004 1301 43 10 3308 4587 367840078 367841377 0.000000e+00 2023.0
44 TraesCS2B01G225100 chr3B 96.498 1085 36 2 3311 4395 178259468 178258386 0.000000e+00 1792.0
45 TraesCS2B01G225100 chr3B 95.175 228 10 1 4675 4902 424124916 424125142 7.850000e-95 359.0
46 TraesCS2B01G225100 chr3B 91.121 214 10 2 4689 4902 434403846 434403642 1.750000e-71 281.0
47 TraesCS2B01G225100 chr3B 80.071 281 27 16 3027 3306 33411054 33411306 1.820000e-41 182.0
48 TraesCS2B01G225100 chr3B 95.745 94 4 0 6704 6797 714106488 714106395 1.430000e-32 152.0
49 TraesCS2B01G225100 chr3B 100.000 29 0 0 4908 4936 751755247 751755275 4.000000e-03 54.7
50 TraesCS2B01G225100 chr7B 93.092 1158 53 12 3786 4934 524617080 524618219 0.000000e+00 1670.0
51 TraesCS2B01G225100 chr7B 100.000 84 0 0 6706 6789 642496222 642496139 1.110000e-33 156.0
52 TraesCS2B01G225100 chr7B 92.381 105 3 1 6689 6788 244219411 244219307 2.390000e-30 145.0
53 TraesCS2B01G225100 chr4B 93.261 1009 65 3 3938 4945 250730270 250729264 0.000000e+00 1483.0
54 TraesCS2B01G225100 chr4B 94.737 95 5 0 6704 6798 113906756 113906662 1.850000e-31 148.0
55 TraesCS2B01G225100 chr4B 92.784 97 5 2 7540 7635 192792751 192792846 1.110000e-28 139.0
56 TraesCS2B01G225100 chr4B 87.931 116 9 4 7524 7635 631527763 631527877 1.860000e-26 132.0
57 TraesCS2B01G225100 chr4B 76.220 164 33 6 179 340 3907862 3907703 1.900000e-11 82.4
58 TraesCS2B01G225100 chr7A 88.636 660 61 11 4247 4902 128902647 128901998 0.000000e+00 791.0
59 TraesCS2B01G225100 chr7A 88.502 661 64 9 4247 4902 726481053 726481706 0.000000e+00 789.0
60 TraesCS2B01G225100 chr1A 84.934 531 47 18 2777 3306 417916428 417916926 2.650000e-139 507.0
61 TraesCS2B01G225100 chr1A 79.281 473 37 32 1960 2403 417915780 417916220 2.930000e-69 274.0
62 TraesCS2B01G225100 chr1A 96.774 93 3 0 6704 6796 12578129 12578037 1.110000e-33 156.0
63 TraesCS2B01G225100 chr1A 97.561 82 2 0 7540 7621 530756579 530756660 3.100000e-29 141.0
64 TraesCS2B01G225100 chr1A 96.429 84 3 0 7540 7623 505489787 505489870 1.110000e-28 139.0
65 TraesCS2B01G225100 chr1A 90.000 110 6 1 6684 6788 399494659 399494550 4.010000e-28 137.0
66 TraesCS2B01G225100 chr1A 94.444 90 3 1 7535 7622 551582255 551582344 4.010000e-28 137.0
67 TraesCS2B01G225100 chr1A 92.708 96 4 2 7540 7635 533694057 533693965 1.440000e-27 135.0
68 TraesCS2B01G225100 chr1A 75.904 166 35 5 179 341 2839831 2839994 6.850000e-11 80.5
69 TraesCS2B01G225100 chr5D 90.133 375 30 3 2783 3153 388858804 388858433 1.610000e-131 481.0
70 TraesCS2B01G225100 chr5D 82.657 542 43 19 2123 2649 388859328 388858823 4.560000e-117 433.0
71 TraesCS2B01G225100 chr5D 85.924 341 37 4 2204 2534 310176250 310175911 3.650000e-93 353.0
72 TraesCS2B01G225100 chr5D 85.876 177 16 6 1960 2135 388859511 388859343 6.560000e-41 180.0
73 TraesCS2B01G225100 chr5D 85.311 177 17 7 1960 2135 310176488 310176320 3.050000e-39 174.0
74 TraesCS2B01G225100 chr5D 95.604 91 1 3 7540 7628 528145878 528145967 8.610000e-30 143.0
75 TraesCS2B01G225100 chr5D 97.561 82 2 0 7540 7621 509426551 509426470 3.100000e-29 141.0
76 TraesCS2B01G225100 chr5D 96.471 85 2 1 7540 7624 128577592 128577675 1.110000e-28 139.0
77 TraesCS2B01G225100 chr5D 92.632 95 5 1 7534 7626 434549400 434549306 1.440000e-27 135.0
78 TraesCS2B01G225100 chr5D 94.382 89 3 1 7535 7621 446918168 446918256 1.440000e-27 135.0
79 TraesCS2B01G225100 chr5D 91.000 100 6 3 7540 7637 482013908 482014006 1.860000e-26 132.0
80 TraesCS2B01G225100 chr3D 89.474 133 7 3 6680 6806 462197527 462197396 2.380000e-35 161.0
81 TraesCS2B01G225100 chr3D 90.323 124 3 5 6676 6791 438431050 438430928 3.980000e-33 154.0
82 TraesCS2B01G225100 chr3D 96.512 86 3 0 7540 7625 302930467 302930382 8.610000e-30 143.0
83 TraesCS2B01G225100 chr3D 94.505 91 3 2 7540 7629 429097589 429097500 1.110000e-28 139.0
84 TraesCS2B01G225100 chr1D 97.778 90 2 0 6704 6793 490029557 490029646 1.110000e-33 156.0
85 TraesCS2B01G225100 chr1D 98.824 85 1 0 6704 6788 466481201 466481117 1.430000e-32 152.0
86 TraesCS2B01G225100 chr1D 97.701 87 2 0 6704 6790 190767364 190767278 5.150000e-32 150.0
87 TraesCS2B01G225100 chr1D 97.701 87 2 0 6704 6790 279100868 279100954 5.150000e-32 150.0
88 TraesCS2B01G225100 chr1D 93.137 102 4 3 6690 6788 180852498 180852397 6.660000e-31 147.0
89 TraesCS2B01G225100 chrUn 94.737 95 5 0 6706 6800 21367833 21367739 1.850000e-31 148.0
90 TraesCS2B01G225100 chrUn 97.674 86 2 0 6704 6789 100242020 100242105 1.850000e-31 148.0
91 TraesCS2B01G225100 chrUn 97.647 85 2 0 6704 6788 50785636 50785720 6.660000e-31 147.0
92 TraesCS2B01G225100 chrUn 96.591 88 3 0 6704 6791 56557322 56557235 6.660000e-31 147.0
93 TraesCS2B01G225100 chrUn 97.647 85 2 0 6704 6788 305213144 305213228 6.660000e-31 147.0
94 TraesCS2B01G225100 chrUn 96.296 81 3 0 7540 7620 101630804 101630884 5.180000e-27 134.0
95 TraesCS2B01G225100 chrUn 95.238 84 4 0 7540 7623 362464958 362465041 5.180000e-27 134.0
96 TraesCS2B01G225100 chrUn 94.186 86 5 0 7536 7621 225564030 225564115 1.860000e-26 132.0
97 TraesCS2B01G225100 chrUn 94.186 86 5 0 7536 7621 237460340 237460255 1.860000e-26 132.0
98 TraesCS2B01G225100 chrUn 94.186 86 5 0 7536 7621 257672056 257671971 1.860000e-26 132.0
99 TraesCS2B01G225100 chrUn 94.186 86 5 0 7536 7621 279682197 279682112 1.860000e-26 132.0
100 TraesCS2B01G225100 chrUn 96.296 81 2 1 7540 7620 320256177 320256098 1.860000e-26 132.0
101 TraesCS2B01G225100 chrUn 96.296 81 2 1 7540 7620 357700827 357700748 1.860000e-26 132.0
102 TraesCS2B01G225100 chrUn 95.122 82 4 0 7540 7621 37028915 37028996 6.700000e-26 130.0
103 TraesCS2B01G225100 chrUn 93.182 88 6 0 6704 6791 79676584 79676497 6.700000e-26 130.0
104 TraesCS2B01G225100 chrUn 92.771 83 6 0 6706 6788 479537887 479537805 4.030000e-23 121.0
105 TraesCS2B01G225100 chrUn 92.771 83 4 2 6707 6788 71546877 71546796 1.450000e-22 119.0
106 TraesCS2B01G225100 chrUn 92.771 83 4 2 6707 6788 79676515 79676596 1.450000e-22 119.0
107 TraesCS2B01G225100 chr4D 97.674 86 2 0 6704 6789 72678763 72678678 1.850000e-31 148.0
108 TraesCS2B01G225100 chr4D 97.674 86 2 0 6704 6789 122272822 122272737 1.850000e-31 148.0
109 TraesCS2B01G225100 chr4D 97.647 85 2 0 6704 6788 54412644 54412560 6.660000e-31 147.0
110 TraesCS2B01G225100 chr4D 97.647 85 2 0 6704 6788 230489554 230489638 6.660000e-31 147.0
111 TraesCS2B01G225100 chr4D 97.619 84 2 0 7540 7623 245478342 245478425 2.390000e-30 145.0
112 TraesCS2B01G225100 chr4D 97.619 84 2 0 7540 7623 282080028 282079945 2.390000e-30 145.0
113 TraesCS2B01G225100 chr4D 95.604 91 3 1 6699 6788 504124156 504124066 2.390000e-30 145.0
114 TraesCS2B01G225100 chr4D 96.429 84 3 0 7540 7623 64347365 64347448 1.110000e-28 139.0
115 TraesCS2B01G225100 chr4D 97.531 81 2 0 7540 7620 99662487 99662407 1.110000e-28 139.0
116 TraesCS2B01G225100 chr4D 96.429 84 3 0 7540 7623 252173784 252173701 1.110000e-28 139.0
117 TraesCS2B01G225100 chr4D 97.531 81 2 0 7540 7620 324227841 324227761 1.110000e-28 139.0
118 TraesCS2B01G225100 chr4D 98.684 76 1 0 7545 7620 352127883 352127808 1.440000e-27 135.0
119 TraesCS2B01G225100 chr4D 96.341 82 3 0 7540 7621 469582352 469582271 1.440000e-27 135.0
120 TraesCS2B01G225100 chr4D 90.000 100 10 0 7540 7639 414221189 414221090 6.700000e-26 130.0
121 TraesCS2B01G225100 chr6D 96.591 88 3 0 6704 6791 35700808 35700721 6.660000e-31 147.0
122 TraesCS2B01G225100 chr6D 97.647 85 2 0 6704 6788 389999710 389999794 6.660000e-31 147.0
123 TraesCS2B01G225100 chr6D 93.814 97 6 0 6704 6800 425086045 425085949 6.660000e-31 147.0
124 TraesCS2B01G225100 chr6D 96.471 85 1 2 7540 7623 1551879 1551796 1.110000e-28 139.0
125 TraesCS2B01G225100 chr6D 95.294 85 4 0 7540 7624 299191267 299191351 1.440000e-27 135.0
126 TraesCS2B01G225100 chr6D 76.506 166 32 7 178 340 57474476 57474637 5.290000e-12 84.2
127 TraesCS2B01G225100 chr6A 97.619 84 2 0 7540 7623 584511366 584511449 2.390000e-30 145.0
128 TraesCS2B01G225100 chr6A 95.506 89 3 1 7540 7628 499008440 499008527 3.100000e-29 141.0
129 TraesCS2B01G225100 chr7D 76.543 162 32 6 181 340 3103474 3103631 5.290000e-12 84.2
130 TraesCS2B01G225100 chr7D 76.543 162 32 6 181 340 3160294 3160137 5.290000e-12 84.2


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 TraesCS2B01G225100 chr2B 214821422 214829652 8230 False 15200.000000 15200 100.000000 1 8231 1 chr2B.!!$F1 8230
1 TraesCS2B01G225100 chr2B 195063284 195064932 1648 True 2455.000000 2455 93.814000 3313 4934 1 chr2B.!!$R1 1621
2 TraesCS2B01G225100 chr2A 167332008 167337815 5807 False 1922.750000 4050 88.625000 585 8140 4 chr2A.!!$F1 7555
3 TraesCS2B01G225100 chr2D 157379888 157386646 6758 False 1880.400000 3738 91.759800 3 8139 5 chr2D.!!$F1 8136
4 TraesCS2B01G225100 chr2D 621824657 621825792 1135 False 329.333333 483 84.196000 1960 3306 3 chr2D.!!$F2 1346
5 TraesCS2B01G225100 chr1B 316257771 316259413 1642 False 2567.000000 2567 95.073000 3313 4935 1 chr1B.!!$F2 1622
6 TraesCS2B01G225100 chr1B 421431071 421432716 1645 False 2449.000000 2449 93.742000 3311 4935 1 chr1B.!!$F3 1624
7 TraesCS2B01G225100 chr1B 327833729 327835804 2075 False 958.000000 961 92.382000 4260 4934 2 chr1B.!!$F4 674
8 TraesCS2B01G225100 chr6B 113650417 113652051 1634 True 2538.000000 2538 94.830000 3312 4934 1 chr6B.!!$R2 1622
9 TraesCS2B01G225100 chr6B 117702295 117703668 1373 True 1797.000000 1797 90.341000 3324 4694 1 chr6B.!!$R3 1370
10 TraesCS2B01G225100 chr6B 124081338 124083517 2179 True 1327.500000 1757 97.325500 3312 4935 2 chr6B.!!$R6 1623
11 TraesCS2B01G225100 chr6B 713797450 713798649 1199 False 371.333333 518 84.028333 1960 3306 3 chr6B.!!$F1 1346
12 TraesCS2B01G225100 chr5B 636986999 636988635 1636 False 2261.000000 2261 91.758000 3312 4933 1 chr5B.!!$F1 1621
13 TraesCS2B01G225100 chr5B 545002990 545004076 1086 True 378.000000 499 86.415333 1960 3153 3 chr5B.!!$R3 1193
14 TraesCS2B01G225100 chr3B 367840078 367841377 1299 False 2023.000000 2023 95.004000 3308 4587 1 chr3B.!!$F2 1279
15 TraesCS2B01G225100 chr3B 178258386 178259468 1082 True 1792.000000 1792 96.498000 3311 4395 1 chr3B.!!$R1 1084
16 TraesCS2B01G225100 chr7B 524617080 524618219 1139 False 1670.000000 1670 93.092000 3786 4934 1 chr7B.!!$F1 1148
17 TraesCS2B01G225100 chr4B 250729264 250730270 1006 True 1483.000000 1483 93.261000 3938 4945 1 chr4B.!!$R3 1007
18 TraesCS2B01G225100 chr7A 128901998 128902647 649 True 791.000000 791 88.636000 4247 4902 1 chr7A.!!$R1 655
19 TraesCS2B01G225100 chr7A 726481053 726481706 653 False 789.000000 789 88.502000 4247 4902 1 chr7A.!!$F1 655
20 TraesCS2B01G225100 chr1A 417915780 417916926 1146 False 390.500000 507 82.107500 1960 3306 2 chr1A.!!$F5 1346
21 TraesCS2B01G225100 chr5D 388858433 388859511 1078 True 364.666667 481 86.222000 1960 3153 3 chr5D.!!$R4 1193
22 TraesCS2B01G225100 chr5D 310175911 310176488 577 True 263.500000 353 85.617500 1960 2534 2 chr5D.!!$R3 574

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
282 283 0.178987 ACCCTAGACCATCGAGCGAT 60.179 55.000 0.00 0.00 34.81 4.58 F
313 315 0.798771 CTAGAACGAGCTGTGACGCC 60.799 60.000 0.00 0.00 0.00 5.68 F
2246 2299 0.321671 TGCTACCTGTGTGCTTCTCC 59.678 55.000 0.00 0.00 0.00 3.71 F
3142 3275 1.196354 CTTTGCTCTTGCCAACTCGAG 59.804 52.381 11.84 11.84 38.71 4.04 F
3950 4103 1.217057 ACCACATGCCCAAGATCCCT 61.217 55.000 0.00 0.00 0.00 4.20 F
4973 7115 1.333258 GCGTGTCAGAAAGAACTGCAC 60.333 52.381 0.00 0.00 39.27 4.57 F
5583 7743 1.133790 GCTAGCATGTCAGGCCAAAAG 59.866 52.381 10.63 0.44 0.00 2.27 F
6059 8223 0.532417 TTGCTGGCATTTTGTGTGGC 60.532 50.000 0.00 0.00 41.99 5.01 F
6917 9112 2.002586 CAGCAGTAATGGAGTGGAACG 58.997 52.381 0.00 0.00 45.86 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 2299 0.327924 TGTGGGCCATCAGTTACCAG 59.672 55.0 10.70 0.00 0.00 4.00 R
2321 2374 0.178068 AGCATACCGCCACTCGATTT 59.822 50.0 0.00 0.00 44.04 2.17 R
3227 3360 0.762418 TTCACAACGACACCCTGGAT 59.238 50.0 0.00 0.00 0.00 3.41 R
4092 4245 2.383245 CTTGGATCGCTACCCGCCAT 62.383 60.0 0.00 0.00 36.73 4.40 R
5145 7305 2.795231 AACATCTGGACAGGACCATG 57.205 50.0 0.00 0.00 39.34 3.66 R
6009 8173 0.879090 GGGTTTGGCACCTAACGAAG 59.121 55.0 7.71 0.00 46.38 3.79 R
7191 9387 0.035458 CAGGTTCAGAGGCGGAACTT 59.965 55.0 15.64 8.48 43.20 2.66 R
7200 9396 0.035881 TTCTGGCAGCAGGTTCAGAG 59.964 55.0 10.34 0.00 37.52 3.35 R
8166 10802 0.038166 TGGCCCTGCAGTCTAAAAGG 59.962 55.0 13.81 5.74 0.00 3.11 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
132 133 0.798776 CACGGGAGAAAGATGTGCAC 59.201 55.000 10.75 10.75 0.00 4.57
147 148 2.224042 TGTGCACAAGTCGATCTCACTT 60.224 45.455 19.28 1.93 34.24 3.16
218 219 6.784031 ACCCAGATCCATATAAAGGTTCATC 58.216 40.000 7.84 0.23 0.00 2.92
282 283 0.178987 ACCCTAGACCATCGAGCGAT 60.179 55.000 0.00 0.00 34.81 4.58
305 306 1.132643 CTAACGCCACTAGAACGAGCT 59.867 52.381 0.00 0.00 0.00 4.09
313 315 0.798771 CTAGAACGAGCTGTGACGCC 60.799 60.000 0.00 0.00 0.00 5.68
325 327 3.103911 GACGCCTCGTTGTCGGTG 61.104 66.667 0.00 0.00 41.37 4.94
391 394 7.790861 AATTTTATTAGAAGCGGTTTTGACG 57.209 32.000 0.00 0.00 0.00 4.35
453 459 2.807967 TGACCAATTCTTCTTGAGCACG 59.192 45.455 0.00 0.00 0.00 5.34
460 466 2.771089 TCTTCTTGAGCACGCAAAGAT 58.229 42.857 7.69 0.00 0.00 2.40
513 519 6.015434 GGGAAAAAGGAGAAATTAGCTTGTGA 60.015 38.462 0.00 0.00 0.00 3.58
561 567 9.981114 CTACAAAAATTGAAACCCTCTACATTT 57.019 29.630 0.00 0.00 0.00 2.32
660 666 3.242518 GAAAGATAAACGCCTTGGCAAC 58.757 45.455 12.45 0.00 0.00 4.17
928 935 5.133830 ACCTTCTCTTTCTTCCCTTGGTTTA 59.866 40.000 0.00 0.00 0.00 2.01
1168 1176 9.314321 TCGAACCTTAGAAATTAGAATCATGTC 57.686 33.333 0.00 0.00 0.00 3.06
1176 1184 7.278875 AGAAATTAGAATCATGTCAGGTCCTC 58.721 38.462 0.00 0.00 0.00 3.71
1177 1185 6.821616 AATTAGAATCATGTCAGGTCCTCT 57.178 37.500 0.00 0.00 0.00 3.69
1179 1187 3.448934 AGAATCATGTCAGGTCCTCTGT 58.551 45.455 0.00 0.00 43.76 3.41
1235 1243 6.423001 GGTTATCGAAGGCGTTATATTTGTCT 59.577 38.462 0.00 0.00 38.98 3.41
1236 1244 7.596248 GGTTATCGAAGGCGTTATATTTGTCTA 59.404 37.037 0.00 0.00 38.98 2.59
1252 1268 4.465632 TGTCTAACTTGTGCGATATGGT 57.534 40.909 0.00 0.00 0.00 3.55
1255 1271 4.630069 GTCTAACTTGTGCGATATGGTTGT 59.370 41.667 0.00 0.00 0.00 3.32
1362 1378 5.387444 CGTTTGAGGCGAGTATAATGATTCG 60.387 44.000 0.00 0.00 36.23 3.34
1406 1422 4.330074 CCGGTTGAGCTGTTTCTTGTATAG 59.670 45.833 0.00 0.00 0.00 1.31
1412 1428 6.230472 TGAGCTGTTTCTTGTATAGCTTTGA 58.770 36.000 0.00 0.00 44.11 2.69
1422 1438 7.268586 TCTTGTATAGCTTTGATCTCCTTCAC 58.731 38.462 0.00 0.00 0.00 3.18
1483 1499 4.802039 GTCTTAGTTGATCGCCATTTACGA 59.198 41.667 0.00 0.00 44.75 3.43
1519 1535 9.227777 ACCTTCCAAGTGTTATTGAATTACTAC 57.772 33.333 0.00 0.00 31.55 2.73
1587 1603 3.563808 TCTGAGTTGGATTTCGTTTGGTG 59.436 43.478 0.00 0.00 0.00 4.17
1638 1654 6.796705 ACGTTTTACTCCATAACTTTCCAG 57.203 37.500 0.00 0.00 0.00 3.86
1777 1793 9.745880 TTTTCTGATACGAGTTATTCTGGATAC 57.254 33.333 0.00 0.00 0.00 2.24
1845 1861 9.824534 GGTAGTTGCAAATTTTTATTTTCATGG 57.175 29.630 4.05 0.00 0.00 3.66
2028 2052 2.294791 AGACTACTCTGTGACTGTGTGC 59.705 50.000 7.32 0.00 0.00 4.57
2246 2299 0.321671 TGCTACCTGTGTGCTTCTCC 59.678 55.000 0.00 0.00 0.00 3.71
2321 2374 9.624697 GCACATTTCTGTATTTCAAATTAGACA 57.375 29.630 0.00 0.00 33.14 3.41
2404 2489 4.038883 TCACAGTCTCTGGATATGCATGAG 59.961 45.833 10.16 7.06 35.51 2.90
2561 2686 4.522689 TGTCTGTGGTGCGTGCGT 62.523 61.111 0.00 0.00 0.00 5.24
2653 2782 3.565482 CAGATTTGGATTATGGTGGGTCG 59.435 47.826 0.00 0.00 0.00 4.79
2815 2944 9.767684 CAATACTCAGCACGTCATTTATTTTTA 57.232 29.630 0.00 0.00 0.00 1.52
3022 3155 7.049754 GGAAACAATCCCATTCAGCAAAATAT 58.950 34.615 0.00 0.00 43.00 1.28
3142 3275 1.196354 CTTTGCTCTTGCCAACTCGAG 59.804 52.381 11.84 11.84 38.71 4.04
3183 3316 8.948631 TCTATGTTTGCTCATACCTTCTTAAG 57.051 34.615 0.00 0.00 0.00 1.85
3184 3317 5.880054 TGTTTGCTCATACCTTCTTAAGC 57.120 39.130 0.00 0.00 0.00 3.09
3185 3318 5.312895 TGTTTGCTCATACCTTCTTAAGCA 58.687 37.500 0.00 0.00 37.93 3.91
3301 3434 7.822334 CCAGGTCTAAACTTACATGAACACATA 59.178 37.037 0.00 0.00 29.13 2.29
3338 3471 1.596934 CGTTGCTAGAAGGAGGGCA 59.403 57.895 0.00 0.00 0.00 5.36
3490 3626 2.917205 AGGCTTACTTGACCCCTAAGT 58.083 47.619 0.00 0.00 41.06 2.24
3499 3635 2.607499 TGACCCCTAAGTAAACGACCA 58.393 47.619 0.00 0.00 0.00 4.02
3632 3771 1.282248 AACCATGACTCGACGCAACG 61.282 55.000 0.00 0.00 0.00 4.10
3950 4103 1.217057 ACCACATGCCCAAGATCCCT 61.217 55.000 0.00 0.00 0.00 4.20
4371 5942 1.453379 GATGGATGGCAGCTGCAGT 60.453 57.895 37.63 25.90 44.36 4.40
4973 7115 1.333258 GCGTGTCAGAAAGAACTGCAC 60.333 52.381 0.00 0.00 39.27 4.57
5091 7251 4.346418 ACCATCTTCCAGTATAGCCTTCAG 59.654 45.833 0.00 0.00 0.00 3.02
5156 7316 5.712152 AAATTCAGTTTCATGGTCCTGTC 57.288 39.130 0.00 0.00 0.00 3.51
5216 7376 2.814097 GCTCCCACTAAGCCTTTTGTGA 60.814 50.000 10.53 0.00 40.86 3.58
5285 7445 8.718102 TCGTTTTTGTTCCCATTTTTAATGAA 57.282 26.923 1.11 0.00 0.00 2.57
5296 7456 8.646900 TCCCATTTTTAATGAATATGGCTAACC 58.353 33.333 2.50 0.00 42.32 2.85
5382 7542 9.520515 CCATATAAGATTGGCATAAGTTAAGGT 57.479 33.333 0.00 0.00 0.00 3.50
5400 7560 7.333672 AGTTAAGGTTAAACAATCCGTGATCTC 59.666 37.037 0.00 0.00 0.00 2.75
5583 7743 1.133790 GCTAGCATGTCAGGCCAAAAG 59.866 52.381 10.63 0.44 0.00 2.27
5690 7850 9.190858 GCTTATGTCTCACTCACAATATCTTAG 57.809 37.037 0.00 0.00 0.00 2.18
5813 7976 9.162764 CTTGTAGCTCCTTAACAATTTAAGCTA 57.837 33.333 0.00 0.00 42.05 3.32
5828 7991 8.398665 CAATTTAAGCTATTAGGTGAACTCCAC 58.601 37.037 0.00 0.00 44.95 4.02
6009 8173 6.756221 TGACAGTTAGAGACTAACTTTTCCC 58.244 40.000 17.80 8.80 36.65 3.97
6059 8223 0.532417 TTGCTGGCATTTTGTGTGGC 60.532 50.000 0.00 0.00 41.99 5.01
6068 8232 4.458642 GGCATTTTGTGTGGCCAATTTAAT 59.541 37.500 7.24 0.89 45.70 1.40
6172 8336 3.798202 CTTGGTACAGTTCCTCCTATGC 58.202 50.000 0.00 0.00 42.39 3.14
6253 8418 2.762535 AACTGATGGACCTAACCGTG 57.237 50.000 0.00 0.00 0.00 4.94
6500 8665 5.873732 AGCTTCGAAATAGTTTTGAGCATC 58.126 37.500 0.00 0.00 34.67 3.91
6637 8813 8.886719 TCTATTTATCATGTAATAGCATGCTGC 58.113 33.333 30.42 16.72 44.20 5.25
6705 8881 8.429641 TGTTTTGTATTCTCATATACTCCCTCC 58.570 37.037 0.00 0.00 33.19 4.30
6706 8882 8.429641 GTTTTGTATTCTCATATACTCCCTCCA 58.570 37.037 0.00 0.00 33.19 3.86
6707 8883 8.561536 TTTGTATTCTCATATACTCCCTCCAA 57.438 34.615 0.00 0.00 33.19 3.53
6708 8884 8.561536 TTGTATTCTCATATACTCCCTCCAAA 57.438 34.615 0.00 0.00 33.19 3.28
6709 8885 8.561536 TGTATTCTCATATACTCCCTCCAAAA 57.438 34.615 0.00 0.00 33.19 2.44
6710 8886 9.170890 TGTATTCTCATATACTCCCTCCAAAAT 57.829 33.333 0.00 0.00 33.19 1.82
6713 8889 9.621239 ATTCTCATATACTCCCTCCAAAATAGA 57.379 33.333 0.00 0.00 0.00 1.98
6714 8890 9.621239 TTCTCATATACTCCCTCCAAAATAGAT 57.379 33.333 0.00 0.00 0.00 1.98
6715 8891 9.040259 TCTCATATACTCCCTCCAAAATAGATG 57.960 37.037 0.00 0.00 0.00 2.90
6716 8892 8.972662 TCATATACTCCCTCCAAAATAGATGA 57.027 34.615 0.00 0.00 0.00 2.92
6717 8893 8.816894 TCATATACTCCCTCCAAAATAGATGAC 58.183 37.037 0.00 0.00 0.00 3.06
6718 8894 8.820831 CATATACTCCCTCCAAAATAGATGACT 58.179 37.037 0.00 0.00 0.00 3.41
6719 8895 5.622346 ACTCCCTCCAAAATAGATGACTC 57.378 43.478 0.00 0.00 0.00 3.36
6720 8896 5.032846 ACTCCCTCCAAAATAGATGACTCA 58.967 41.667 0.00 0.00 0.00 3.41
6721 8897 5.488919 ACTCCCTCCAAAATAGATGACTCAA 59.511 40.000 0.00 0.00 0.00 3.02
6722 8898 5.745227 TCCCTCCAAAATAGATGACTCAAC 58.255 41.667 0.00 0.00 0.00 3.18
6723 8899 5.488919 TCCCTCCAAAATAGATGACTCAACT 59.511 40.000 0.00 0.00 0.00 3.16
6724 8900 6.012508 TCCCTCCAAAATAGATGACTCAACTT 60.013 38.462 0.00 0.00 0.00 2.66
6725 8901 6.660949 CCCTCCAAAATAGATGACTCAACTTT 59.339 38.462 0.00 0.00 0.00 2.66
6726 8902 7.362401 CCCTCCAAAATAGATGACTCAACTTTG 60.362 40.741 0.00 0.00 0.00 2.77
6727 8903 7.175641 CCTCCAAAATAGATGACTCAACTTTGT 59.824 37.037 0.00 0.00 0.00 2.83
6728 8904 9.219603 CTCCAAAATAGATGACTCAACTTTGTA 57.780 33.333 0.00 0.00 0.00 2.41
6729 8905 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
6730 8906 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
6761 8937 7.797038 AGTACAAAGTTAGTACAAAGTTGGG 57.203 36.000 6.30 0.00 43.24 4.12
6762 8938 7.341030 AGTACAAAGTTAGTACAAAGTTGGGT 58.659 34.615 6.30 0.00 43.24 4.51
6763 8939 6.688637 ACAAAGTTAGTACAAAGTTGGGTC 57.311 37.500 0.00 0.00 0.00 4.46
6764 8940 6.181908 ACAAAGTTAGTACAAAGTTGGGTCA 58.818 36.000 0.00 0.00 0.00 4.02
6765 8941 6.831868 ACAAAGTTAGTACAAAGTTGGGTCAT 59.168 34.615 0.00 0.00 0.00 3.06
6766 8942 7.012989 ACAAAGTTAGTACAAAGTTGGGTCATC 59.987 37.037 0.00 0.00 0.00 2.92
6767 8943 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
6768 8944 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
6769 8945 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
6770 8946 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
6771 8947 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
6772 8948 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
6773 8949 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
6774 8950 7.942341 AGTACAAAGTTGGGTCATCTATTTTGA 59.058 33.333 0.00 0.00 0.00 2.69
6775 8951 7.595819 ACAAAGTTGGGTCATCTATTTTGAA 57.404 32.000 0.00 0.00 0.00 2.69
6776 8952 8.017418 ACAAAGTTGGGTCATCTATTTTGAAA 57.983 30.769 0.00 0.00 0.00 2.69
6777 8953 7.926018 ACAAAGTTGGGTCATCTATTTTGAAAC 59.074 33.333 0.00 0.00 0.00 2.78
6778 8954 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
6779 8955 5.183140 AGTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
6780 8956 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
6781 8957 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
6782 8958 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
6783 8959 4.335594 GGTCATCTATTTTGAAACGGAGGG 59.664 45.833 0.00 0.00 0.00 4.30
6784 8960 5.183228 GTCATCTATTTTGAAACGGAGGGA 58.817 41.667 0.00 0.00 0.00 4.20
6785 8961 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
6797 8973 2.910977 ACGGAGGGAGTATTTTCCAACT 59.089 45.455 0.00 0.00 39.09 3.16
6860 9042 8.996651 TGATTAGTTGTAGATAGACTGATGGA 57.003 34.615 0.00 0.00 0.00 3.41
6861 9043 9.072375 TGATTAGTTGTAGATAGACTGATGGAG 57.928 37.037 0.00 0.00 0.00 3.86
6863 9045 4.586841 AGTTGTAGATAGACTGATGGAGGC 59.413 45.833 0.00 0.00 0.00 4.70
6881 9074 3.470709 AGGCTGGTTATGATTGATGACG 58.529 45.455 0.00 0.00 0.00 4.35
6917 9112 2.002586 CAGCAGTAATGGAGTGGAACG 58.997 52.381 0.00 0.00 45.86 3.95
6929 9124 5.299949 TGGAGTGGAACGATGATTATGATG 58.700 41.667 0.00 0.00 45.86 3.07
6981 9177 7.656412 TGTTTTTGCTTAGCTTGATGTTATCA 58.344 30.769 5.60 0.00 37.55 2.15
7029 9225 8.579863 CATTTCCCCTAAATATGAATTGTCCTC 58.420 37.037 0.00 0.00 35.54 3.71
7056 9252 2.305927 GGGGAAGAAGTGGAATCTGTCA 59.694 50.000 0.00 0.00 0.00 3.58
7074 9270 6.169094 TCTGTCATTCTCTTTGATCTGGAAC 58.831 40.000 0.00 0.00 0.00 3.62
7189 9385 3.309138 CAGCATGAAGTCATCAGCTACAC 59.691 47.826 0.00 0.00 42.53 2.90
7191 9387 4.403752 AGCATGAAGTCATCAGCTACACTA 59.596 41.667 0.00 0.00 42.53 2.74
7200 9396 1.203994 TCAGCTACACTAAGTTCCGCC 59.796 52.381 0.00 0.00 0.00 6.13
7216 9412 2.752358 CCTCTGAACCTGCTGCCA 59.248 61.111 0.00 0.00 0.00 4.92
7233 9432 7.039923 CCTGCTGCCAGAATATCAAATTAATCT 60.040 37.037 0.00 0.00 41.77 2.40
7252 9451 0.179020 TAGCCAGGGCATTTCATCCG 60.179 55.000 13.63 0.00 44.88 4.18
7267 9479 7.524912 CATTTCATCCGGACAGATATTCAATC 58.475 38.462 6.12 0.00 0.00 2.67
7434 9646 2.674796 AGAACCGCTGTCTGTATTCC 57.325 50.000 0.00 0.00 0.00 3.01
7536 10105 2.676076 GCAAGTGTAATGTTGGCCTTG 58.324 47.619 3.32 0.00 34.03 3.61
7537 10106 2.035832 GCAAGTGTAATGTTGGCCTTGT 59.964 45.455 3.32 0.00 33.57 3.16
7538 10107 3.254657 GCAAGTGTAATGTTGGCCTTGTA 59.745 43.478 3.32 0.00 33.57 2.41
7539 10108 4.794169 CAAGTGTAATGTTGGCCTTGTAC 58.206 43.478 3.32 0.00 0.00 2.90
7540 10109 3.418047 AGTGTAATGTTGGCCTTGTACC 58.582 45.455 3.32 0.00 0.00 3.34
7541 10110 2.490509 GTGTAATGTTGGCCTTGTACCC 59.509 50.000 3.32 0.00 0.00 3.69
7542 10111 2.377193 TGTAATGTTGGCCTTGTACCCT 59.623 45.455 3.32 0.00 0.00 4.34
7543 10112 2.215942 AATGTTGGCCTTGTACCCTC 57.784 50.000 3.32 0.00 0.00 4.30
7544 10113 0.331616 ATGTTGGCCTTGTACCCTCC 59.668 55.000 3.32 0.00 0.00 4.30
7545 10114 1.376812 GTTGGCCTTGTACCCTCCG 60.377 63.158 3.32 0.00 0.00 4.63
7546 10115 1.844289 TTGGCCTTGTACCCTCCGT 60.844 57.895 3.32 0.00 0.00 4.69
7547 10116 0.544833 TTGGCCTTGTACCCTCCGTA 60.545 55.000 3.32 0.00 0.00 4.02
7548 10117 0.544833 TGGCCTTGTACCCTCCGTAA 60.545 55.000 3.32 0.00 0.00 3.18
7549 10118 0.614812 GGCCTTGTACCCTCCGTAAA 59.385 55.000 0.00 0.00 0.00 2.01
7550 10119 1.406477 GGCCTTGTACCCTCCGTAAAG 60.406 57.143 0.00 0.00 0.00 1.85
7551 10120 1.551883 GCCTTGTACCCTCCGTAAAGA 59.448 52.381 0.00 0.00 0.00 2.52
7552 10121 2.027837 GCCTTGTACCCTCCGTAAAGAA 60.028 50.000 0.00 0.00 0.00 2.52
7553 10122 3.557686 GCCTTGTACCCTCCGTAAAGAAA 60.558 47.826 0.00 0.00 0.00 2.52
7554 10123 4.840271 CCTTGTACCCTCCGTAAAGAAAT 58.160 43.478 0.00 0.00 0.00 2.17
7555 10124 5.627503 GCCTTGTACCCTCCGTAAAGAAATA 60.628 44.000 0.00 0.00 0.00 1.40
7556 10125 6.589135 CCTTGTACCCTCCGTAAAGAAATAT 58.411 40.000 0.00 0.00 0.00 1.28
7557 10126 7.687592 GCCTTGTACCCTCCGTAAAGAAATATA 60.688 40.741 0.00 0.00 0.00 0.86
7558 10127 8.206189 CCTTGTACCCTCCGTAAAGAAATATAA 58.794 37.037 0.00 0.00 0.00 0.98
7559 10128 9.257651 CTTGTACCCTCCGTAAAGAAATATAAG 57.742 37.037 0.00 0.00 0.00 1.73
7560 10129 8.537728 TGTACCCTCCGTAAAGAAATATAAGA 57.462 34.615 0.00 0.00 0.00 2.10
7561 10130 8.636213 TGTACCCTCCGTAAAGAAATATAAGAG 58.364 37.037 0.00 0.00 0.00 2.85
7562 10131 6.522946 ACCCTCCGTAAAGAAATATAAGAGC 58.477 40.000 0.00 0.00 0.00 4.09
7563 10132 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
7564 10133 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
7565 10134 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
7566 10135 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
7567 10136 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
7568 10137 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
7569 10138 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
7581 10150 9.900710 ATAAGAGCGTTTAGATCACTAATGTAG 57.099 33.333 0.00 0.00 38.23 2.74
7582 10151 7.336161 AGAGCGTTTAGATCACTAATGTAGT 57.664 36.000 0.00 0.00 38.23 2.73
7596 10165 7.336161 ACTAATGTAGTGATCTAAACGCTCT 57.664 36.000 0.00 0.00 37.69 4.09
7597 10166 7.773149 ACTAATGTAGTGATCTAAACGCTCTT 58.227 34.615 0.00 0.00 37.69 2.85
7598 10167 8.900781 ACTAATGTAGTGATCTAAACGCTCTTA 58.099 33.333 0.00 0.00 37.69 2.10
7599 10168 9.900710 CTAATGTAGTGATCTAAACGCTCTTAT 57.099 33.333 0.00 0.00 0.00 1.73
7614 10183 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
7615 10184 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
7616 10185 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
7687 10256 2.042686 TGTGCCTACCATCTTGATGC 57.957 50.000 5.16 0.00 0.00 3.91
7703 10272 3.202097 TGATGCTGTCGTTTTTGTCTCA 58.798 40.909 0.00 0.00 0.00 3.27
7813 10382 1.448540 CCAGATGGCACGTCAGGAC 60.449 63.158 0.00 0.00 0.00 3.85
7815 10386 0.320683 CAGATGGCACGTCAGGACAA 60.321 55.000 0.00 0.00 0.00 3.18
7877 10494 4.423625 ACTCTTTAGTGAGGTTGCAGTT 57.576 40.909 0.00 0.00 38.32 3.16
7900 10517 3.766545 TGTTCTGCTTATTTGGAGGCTT 58.233 40.909 0.00 0.00 0.00 4.35
7908 10540 1.028868 ATTTGGAGGCTTGAGCGAGC 61.029 55.000 0.95 0.95 43.26 5.03
7913 10545 2.046892 GGCTTGAGCGAGCTTGGA 60.047 61.111 9.43 0.00 42.32 3.53
7914 10546 2.394563 GGCTTGAGCGAGCTTGGAC 61.395 63.158 9.43 0.00 42.32 4.02
7915 10547 1.375268 GCTTGAGCGAGCTTGGACT 60.375 57.895 2.37 0.00 39.57 3.85
7916 10548 1.357991 GCTTGAGCGAGCTTGGACTC 61.358 60.000 2.37 2.42 39.57 3.36
7917 10549 0.246086 CTTGAGCGAGCTTGGACTCT 59.754 55.000 2.37 0.00 34.35 3.24
7918 10550 0.681733 TTGAGCGAGCTTGGACTCTT 59.318 50.000 2.37 0.00 34.35 2.85
7919 10551 0.244994 TGAGCGAGCTTGGACTCTTC 59.755 55.000 2.37 0.00 34.35 2.87
7920 10552 0.459411 GAGCGAGCTTGGACTCTTCC 60.459 60.000 2.37 0.00 43.19 3.46
7931 10563 3.817709 GGACTCTTCCATCTTGAGAGG 57.182 52.381 4.81 0.00 42.30 3.69
7932 10564 2.158971 GGACTCTTCCATCTTGAGAGGC 60.159 54.545 4.81 1.08 43.39 4.70
7933 10565 2.499289 GACTCTTCCATCTTGAGAGGCA 59.501 50.000 0.75 0.00 43.55 4.75
7934 10566 2.500910 ACTCTTCCATCTTGAGAGGCAG 59.499 50.000 4.81 0.00 40.89 4.85
7935 10567 2.765135 CTCTTCCATCTTGAGAGGCAGA 59.235 50.000 0.00 0.00 34.63 4.26
7936 10568 3.382278 TCTTCCATCTTGAGAGGCAGAT 58.618 45.455 0.00 0.00 0.00 2.90
7937 10569 3.779183 TCTTCCATCTTGAGAGGCAGATT 59.221 43.478 0.00 0.00 0.00 2.40
7938 10570 3.555527 TCCATCTTGAGAGGCAGATTG 57.444 47.619 0.00 0.00 0.00 2.67
7939 10571 3.109928 TCCATCTTGAGAGGCAGATTGA 58.890 45.455 0.00 0.00 0.00 2.57
7947 10579 1.703438 GAGGCAGATTGAGCTGTGCG 61.703 60.000 0.00 0.00 36.34 5.34
7957 10589 3.058160 GCTGTGCGCTCATGGGTT 61.058 61.111 13.20 0.00 35.14 4.11
8003 10636 5.614013 GCGTGTGAGGTTTATGTTTGTCTAC 60.614 44.000 0.00 0.00 0.00 2.59
8027 10660 6.692681 ACAATCGTCATGTTGCTTAATTATGC 59.307 34.615 14.72 14.72 0.00 3.14
8045 10678 8.686739 AATTATGCTATATTGAGGTAGGGTCT 57.313 34.615 0.00 0.00 0.00 3.85
8046 10679 8.686739 ATTATGCTATATTGAGGTAGGGTCTT 57.313 34.615 0.00 0.00 0.00 3.01
8047 10680 8.506196 TTATGCTATATTGAGGTAGGGTCTTT 57.494 34.615 0.00 0.00 0.00 2.52
8048 10681 6.824958 TGCTATATTGAGGTAGGGTCTTTT 57.175 37.500 0.00 0.00 0.00 2.27
8049 10682 7.208064 TGCTATATTGAGGTAGGGTCTTTTT 57.792 36.000 0.00 0.00 0.00 1.94
8080 10713 7.171630 AGTGATTAAACACCTACTACTCCTG 57.828 40.000 11.83 0.00 41.12 3.86
8084 10717 8.475639 TGATTAAACACCTACTACTCCTGAATC 58.524 37.037 0.00 0.00 0.00 2.52
8116 10752 0.670854 GTTCAGGGAGGAAGTGCGTC 60.671 60.000 0.00 0.00 0.00 5.19
8176 10812 8.164057 AGGTGATCCTTTTATCCTTTTAGACT 57.836 34.615 0.00 0.00 42.12 3.24
8177 10813 8.049721 AGGTGATCCTTTTATCCTTTTAGACTG 58.950 37.037 0.00 0.00 42.12 3.51
8178 10814 7.201741 GGTGATCCTTTTATCCTTTTAGACTGC 60.202 40.741 0.00 0.00 0.00 4.40
8179 10815 7.336931 GTGATCCTTTTATCCTTTTAGACTGCA 59.663 37.037 0.00 0.00 0.00 4.41
8180 10816 7.554118 TGATCCTTTTATCCTTTTAGACTGCAG 59.446 37.037 13.48 13.48 0.00 4.41
8181 10817 6.180472 TCCTTTTATCCTTTTAGACTGCAGG 58.820 40.000 19.93 0.00 0.00 4.85
8182 10818 5.358160 CCTTTTATCCTTTTAGACTGCAGGG 59.642 44.000 19.93 7.65 0.00 4.45
8183 10819 2.426842 ATCCTTTTAGACTGCAGGGC 57.573 50.000 19.93 9.79 0.00 5.19
8184 10820 0.328258 TCCTTTTAGACTGCAGGGCC 59.672 55.000 19.93 6.79 0.00 5.80
8185 10821 0.038166 CCTTTTAGACTGCAGGGCCA 59.962 55.000 19.93 0.00 0.00 5.36
8186 10822 1.341383 CCTTTTAGACTGCAGGGCCAT 60.341 52.381 19.93 0.00 0.00 4.40
8187 10823 2.019984 CTTTTAGACTGCAGGGCCATC 58.980 52.381 19.93 5.87 0.00 3.51
8188 10824 0.991146 TTTAGACTGCAGGGCCATCA 59.009 50.000 19.93 1.30 0.00 3.07
8189 10825 0.991146 TTAGACTGCAGGGCCATCAA 59.009 50.000 19.93 0.00 0.00 2.57
8190 10826 0.991146 TAGACTGCAGGGCCATCAAA 59.009 50.000 19.93 0.00 0.00 2.69
8191 10827 0.112995 AGACTGCAGGGCCATCAAAA 59.887 50.000 19.93 0.00 0.00 2.44
8192 10828 1.188863 GACTGCAGGGCCATCAAAAT 58.811 50.000 19.93 0.00 0.00 1.82
8193 10829 1.551883 GACTGCAGGGCCATCAAAATT 59.448 47.619 19.93 0.00 0.00 1.82
8194 10830 1.980036 ACTGCAGGGCCATCAAAATTT 59.020 42.857 19.93 0.00 0.00 1.82
8195 10831 2.289819 ACTGCAGGGCCATCAAAATTTG 60.290 45.455 19.93 0.00 0.00 2.32
8196 10832 1.976404 TGCAGGGCCATCAAAATTTGA 59.024 42.857 11.10 11.10 45.01 2.69
8197 10833 2.371179 TGCAGGGCCATCAAAATTTGAA 59.629 40.909 12.75 0.00 43.95 2.69
8198 10834 3.009253 TGCAGGGCCATCAAAATTTGAAT 59.991 39.130 12.75 0.00 43.95 2.57
8199 10835 4.011698 GCAGGGCCATCAAAATTTGAATT 58.988 39.130 12.75 0.00 43.95 2.17
8200 10836 4.460034 GCAGGGCCATCAAAATTTGAATTT 59.540 37.500 12.75 0.00 43.95 1.82
8201 10837 5.047872 GCAGGGCCATCAAAATTTGAATTTT 60.048 36.000 12.75 8.27 46.42 1.82
8225 10861 7.561021 TGAAACATTCAACTGCTAAAGTACA 57.439 32.000 0.00 0.00 38.56 2.90
8226 10862 7.414436 TGAAACATTCAACTGCTAAAGTACAC 58.586 34.615 0.00 0.00 38.56 2.90
8227 10863 5.941948 ACATTCAACTGCTAAAGTACACC 57.058 39.130 0.00 0.00 38.56 4.16
8228 10864 5.373222 ACATTCAACTGCTAAAGTACACCA 58.627 37.500 0.00 0.00 38.56 4.17
8229 10865 5.238650 ACATTCAACTGCTAAAGTACACCAC 59.761 40.000 0.00 0.00 38.56 4.16
8230 10866 3.735591 TCAACTGCTAAAGTACACCACC 58.264 45.455 0.00 0.00 38.56 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 4.460731 TGATCCATGCGGTATTTTGTCAAA 59.539 37.500 0.00 0.00 0.00 2.69
71 72 3.953612 ACATGATCCATGCGGTATTTTGT 59.046 39.130 0.00 0.00 44.80 2.83
132 133 9.959775 GTAGATTTTTAAAGTGAGATCGACTTG 57.040 33.333 12.34 0.00 33.85 3.16
188 189 7.652554 ACCTTTATATGGATCTGGGTCTTTTT 58.347 34.615 0.00 0.00 0.00 1.94
199 200 9.730705 TGATTCTGATGAACCTTTATATGGATC 57.269 33.333 0.00 0.00 34.71 3.36
218 219 4.202040 TGTTTGAGGTGCTTTGTGATTCTG 60.202 41.667 0.00 0.00 0.00 3.02
262 263 0.471191 TCGCTCGATGGTCTAGGGTA 59.529 55.000 0.00 0.00 0.00 3.69
266 267 1.876799 AGTGATCGCTCGATGGTCTAG 59.123 52.381 9.70 0.00 34.60 2.43
282 283 2.153645 TCGTTCTAGTGGCGTTAGTGA 58.846 47.619 0.00 0.00 0.00 3.41
292 293 1.607713 CGTCACAGCTCGTTCTAGTG 58.392 55.000 0.00 0.00 0.00 2.74
305 306 2.354188 CGACAACGAGGCGTCACA 60.354 61.111 7.26 0.00 46.08 3.58
313 315 2.432628 GGGAGCACCGACAACGAG 60.433 66.667 0.00 0.00 42.66 4.18
366 368 8.505625 ACGTCAAAACCGCTTCTAATAAAATTA 58.494 29.630 0.00 0.00 0.00 1.40
453 459 8.311650 ACTGTCGGTTATGATAATATCTTTGC 57.688 34.615 1.66 0.00 0.00 3.68
513 519 9.263446 TGTAGTCAGTACTGGGTATTTATTTCT 57.737 33.333 22.48 6.84 36.36 2.52
660 666 1.214373 ACAAACGCATTGCTTTGCCG 61.214 50.000 22.36 10.25 43.13 5.69
986 994 1.103398 CATCATGAACCCCGGGCTTC 61.103 60.000 20.03 20.03 0.00 3.86
993 1001 0.034186 TGTGCTCCATCATGAACCCC 60.034 55.000 0.00 0.00 0.00 4.95
1214 1222 7.208080 AGTTAGACAAATATAACGCCTTCGAT 58.792 34.615 0.00 0.00 37.54 3.59
1235 1243 4.570930 TCACAACCATATCGCACAAGTTA 58.429 39.130 0.00 0.00 0.00 2.24
1236 1244 3.407698 TCACAACCATATCGCACAAGTT 58.592 40.909 0.00 0.00 0.00 2.66
1252 1268 1.866601 CTCAGTGACACGCATTCACAA 59.133 47.619 12.59 2.06 45.00 3.33
1255 1271 0.392706 ACCTCAGTGACACGCATTCA 59.607 50.000 0.00 0.00 0.00 2.57
1362 1378 4.666237 GGTGTTCTAATTCATGAAGCAGC 58.334 43.478 14.54 10.62 0.00 5.25
1406 1422 3.823304 ACAAAGGTGAAGGAGATCAAAGC 59.177 43.478 0.00 0.00 0.00 3.51
1412 1428 5.053978 ACAGAAACAAAGGTGAAGGAGAT 57.946 39.130 0.00 0.00 0.00 2.75
1422 1438 4.714632 TCTACCTCCAACAGAAACAAAGG 58.285 43.478 0.00 0.00 0.00 3.11
1483 1499 5.520748 ACACTTGGAAGGTAAATCTCCAT 57.479 39.130 0.00 0.00 0.00 3.41
1587 1603 0.451783 CAAACGCCATCTGCCCTAAC 59.548 55.000 0.00 0.00 36.24 2.34
1777 1793 6.959361 ACCGCAATAAGTAGCATTTCTATTG 58.041 36.000 0.00 0.00 0.00 1.90
1845 1861 3.578688 GGATTCCAAACATTGTGCTGTC 58.421 45.455 0.00 0.00 0.00 3.51
2246 2299 0.327924 TGTGGGCCATCAGTTACCAG 59.672 55.000 10.70 0.00 0.00 4.00
2321 2374 0.178068 AGCATACCGCCACTCGATTT 59.822 50.000 0.00 0.00 44.04 2.17
2404 2489 7.011295 TCACCATTCAAAAAGCAACATTTTCTC 59.989 33.333 0.00 0.00 31.25 2.87
2488 2606 6.728411 TGAGTCTCACATCTACCTTAACCTA 58.272 40.000 0.00 0.00 0.00 3.08
2561 2686 3.429492 TGGTTTATCCATGCTGCAAGAA 58.571 40.909 6.36 0.00 41.93 2.52
2653 2782 1.416772 GGATGAAGCCACCCCTAGTAC 59.583 57.143 0.00 0.00 0.00 2.73
2793 2922 7.197071 TGTAAAAATAAATGACGTGCTGAGT 57.803 32.000 0.00 0.00 0.00 3.41
2815 2944 2.282040 GTGCAAGCCAGAGCCTGT 60.282 61.111 0.00 0.00 41.25 4.00
3022 3155 4.521639 AGCTTCAAGATGAACTTCATGCAA 59.478 37.500 9.08 0.00 37.20 4.08
3227 3360 0.762418 TTCACAACGACACCCTGGAT 59.238 50.000 0.00 0.00 0.00 3.41
3235 3368 6.627395 AATTTTAGGTGATTCACAACGACA 57.373 33.333 18.09 0.00 41.74 4.35
3278 3411 8.995220 TGTTATGTGTTCATGTAAGTTTAGACC 58.005 33.333 0.00 0.00 35.70 3.85
3301 3434 5.163794 GCAACGCCATAACAGTAACTATGTT 60.164 40.000 0.00 0.00 43.15 2.71
3306 3439 3.053831 AGCAACGCCATAACAGTAACT 57.946 42.857 0.00 0.00 0.00 2.24
3322 3455 0.902984 TCGTGCCCTCCTTCTAGCAA 60.903 55.000 0.00 0.00 36.91 3.91
3376 3512 2.816777 GAAATCCCTTCCCTCTTGCT 57.183 50.000 0.00 0.00 0.00 3.91
3529 3666 1.218844 ACGTAATGGGCCTAATGGGT 58.781 50.000 4.53 0.00 37.43 4.51
3632 3771 5.233476 GCTTGTTTTTAGGTGTTAGGTTTGC 59.767 40.000 0.00 0.00 0.00 3.68
3950 4103 3.396911 GATCTCGTCCGCTGCGTCA 62.397 63.158 21.59 3.88 0.00 4.35
4092 4245 2.383245 CTTGGATCGCTACCCGCCAT 62.383 60.000 0.00 0.00 36.73 4.40
4548 6678 3.147595 CCGGGATCCTCTGTCGCA 61.148 66.667 12.58 0.00 0.00 5.10
4746 6878 2.927856 TTCCCTCTTGCTCGGCCA 60.928 61.111 2.24 0.00 0.00 5.36
4752 6884 2.816777 GAAATCCCTTCCCTCTTGCT 57.183 50.000 0.00 0.00 0.00 3.91
5145 7305 2.795231 AACATCTGGACAGGACCATG 57.205 50.000 0.00 0.00 39.34 3.66
5156 7316 6.879276 ATGCATTCAAGATCTAACATCTGG 57.121 37.500 0.00 0.00 0.00 3.86
5309 7469 7.988028 AGTCAAACTTATAAGCCAGATAAGTCC 59.012 37.037 12.54 5.54 45.23 3.85
5382 7542 5.789521 TCACTGAGATCACGGATTGTTTAA 58.210 37.500 5.93 0.00 0.00 1.52
5527 7687 5.703592 TGTATTAACCTGAATCAGTTGCGTT 59.296 36.000 9.63 8.42 0.00 4.84
5583 7743 3.274288 CAATTCTGCCAACTCCTCTACC 58.726 50.000 0.00 0.00 0.00 3.18
5690 7850 4.674281 AGTAGCAGTATTGTAGGGAAGC 57.326 45.455 0.00 0.00 0.00 3.86
5892 8056 5.327732 AGGAAAGTCATGGTCACATTTCAT 58.672 37.500 0.00 0.00 34.35 2.57
6009 8173 0.879090 GGGTTTGGCACCTAACGAAG 59.121 55.000 7.71 0.00 46.38 3.79
6059 8223 4.609301 TCCAGAAGGGGACATTAAATTGG 58.391 43.478 0.00 0.00 37.22 3.16
6068 8232 2.118403 AGAACTTCCAGAAGGGGACA 57.882 50.000 11.87 0.00 42.53 4.02
6233 8397 2.370849 ACACGGTTAGGTCCATCAGTTT 59.629 45.455 0.00 0.00 0.00 2.66
6235 8399 1.640917 ACACGGTTAGGTCCATCAGT 58.359 50.000 0.00 0.00 0.00 3.41
6630 8806 2.647337 GCGATTATCACTTGCAGCATG 58.353 47.619 6.74 6.74 40.87 4.06
6637 8813 1.299541 AAGCCCGCGATTATCACTTG 58.700 50.000 8.23 0.00 0.00 3.16
6696 8872 6.202331 TGAGTCATCTATTTTGGAGGGAGTA 58.798 40.000 0.00 0.00 0.00 2.59
6697 8873 5.032846 TGAGTCATCTATTTTGGAGGGAGT 58.967 41.667 0.00 0.00 0.00 3.85
6698 8874 5.620738 TGAGTCATCTATTTTGGAGGGAG 57.379 43.478 0.00 0.00 0.00 4.30
6699 8875 5.488919 AGTTGAGTCATCTATTTTGGAGGGA 59.511 40.000 1.70 0.00 0.00 4.20
6700 8876 5.749462 AGTTGAGTCATCTATTTTGGAGGG 58.251 41.667 1.70 0.00 0.00 4.30
6701 8877 7.175641 ACAAAGTTGAGTCATCTATTTTGGAGG 59.824 37.037 14.35 0.00 40.00 4.30
6702 8878 8.103948 ACAAAGTTGAGTCATCTATTTTGGAG 57.896 34.615 14.35 1.25 40.00 3.86
6703 8879 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
6704 8880 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
6735 8911 9.328845 CCCAACTTTGTACTAACTTTGTACTAA 57.671 33.333 12.73 10.75 40.44 2.24
6736 8912 8.485392 ACCCAACTTTGTACTAACTTTGTACTA 58.515 33.333 12.73 4.86 40.44 1.82
6737 8913 7.341030 ACCCAACTTTGTACTAACTTTGTACT 58.659 34.615 12.73 0.00 40.44 2.73
6738 8914 7.280652 TGACCCAACTTTGTACTAACTTTGTAC 59.719 37.037 6.58 6.58 40.27 2.90
6739 8915 7.337167 TGACCCAACTTTGTACTAACTTTGTA 58.663 34.615 0.00 0.00 0.00 2.41
6740 8916 6.181908 TGACCCAACTTTGTACTAACTTTGT 58.818 36.000 0.00 0.00 0.00 2.83
6741 8917 6.687081 TGACCCAACTTTGTACTAACTTTG 57.313 37.500 0.00 0.00 0.00 2.77
6742 8918 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
6743 8919 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
6744 8920 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
6745 8921 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
6746 8922 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
6747 8923 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
6748 8924 7.942341 TCAAAATAGATGACCCAACTTTGTACT 59.058 33.333 0.00 0.00 0.00 2.73
6749 8925 8.106247 TCAAAATAGATGACCCAACTTTGTAC 57.894 34.615 0.00 0.00 0.00 2.90
6750 8926 8.698973 TTCAAAATAGATGACCCAACTTTGTA 57.301 30.769 0.00 0.00 0.00 2.41
6751 8927 7.595819 TTCAAAATAGATGACCCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
6752 8928 7.114811 CGTTTCAAAATAGATGACCCAACTTTG 59.885 37.037 0.00 0.00 0.00 2.77
6753 8929 7.145323 CGTTTCAAAATAGATGACCCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
6754 8930 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
6755 8931 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
6756 8932 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
6757 8933 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
6758 8934 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
6759 8935 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
6760 8936 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
6761 8937 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
6762 8938 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
6763 8939 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
6764 8940 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
6765 8941 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
6766 8942 7.625828 AAATACTCCCTCCGTTTCAAAATAG 57.374 36.000 0.00 0.00 0.00 1.73
6767 8943 7.121611 GGAAAATACTCCCTCCGTTTCAAAATA 59.878 37.037 0.00 0.00 0.00 1.40
6768 8944 6.071560 GGAAAATACTCCCTCCGTTTCAAAAT 60.072 38.462 0.00 0.00 0.00 1.82
6769 8945 5.242171 GGAAAATACTCCCTCCGTTTCAAAA 59.758 40.000 0.00 0.00 0.00 2.44
6770 8946 4.763279 GGAAAATACTCCCTCCGTTTCAAA 59.237 41.667 0.00 0.00 0.00 2.69
6771 8947 4.202482 TGGAAAATACTCCCTCCGTTTCAA 60.202 41.667 0.00 0.00 34.22 2.69
6772 8948 3.328343 TGGAAAATACTCCCTCCGTTTCA 59.672 43.478 0.00 0.00 34.22 2.69
6773 8949 3.946606 TGGAAAATACTCCCTCCGTTTC 58.053 45.455 0.00 0.00 34.22 2.78
6774 8950 4.077108 GTTGGAAAATACTCCCTCCGTTT 58.923 43.478 0.00 0.00 34.22 3.60
6775 8951 3.329814 AGTTGGAAAATACTCCCTCCGTT 59.670 43.478 0.00 0.00 34.22 4.44
6776 8952 2.910977 AGTTGGAAAATACTCCCTCCGT 59.089 45.455 0.00 0.00 34.22 4.69
6777 8953 3.055385 TCAGTTGGAAAATACTCCCTCCG 60.055 47.826 0.00 0.00 34.22 4.63
6778 8954 4.262617 GTCAGTTGGAAAATACTCCCTCC 58.737 47.826 0.00 0.00 34.22 4.30
6779 8955 4.906618 TGTCAGTTGGAAAATACTCCCTC 58.093 43.478 0.00 0.00 34.22 4.30
6780 8956 4.993705 TGTCAGTTGGAAAATACTCCCT 57.006 40.909 0.00 0.00 34.22 4.20
6781 8957 6.590234 ATTTGTCAGTTGGAAAATACTCCC 57.410 37.500 0.00 0.00 34.22 4.30
6782 8958 9.406828 GTTAATTTGTCAGTTGGAAAATACTCC 57.593 33.333 0.00 0.00 35.88 3.85
6783 8959 9.406828 GGTTAATTTGTCAGTTGGAAAATACTC 57.593 33.333 0.00 0.00 0.00 2.59
6784 8960 8.919145 TGGTTAATTTGTCAGTTGGAAAATACT 58.081 29.630 0.00 0.00 0.00 2.12
6785 8961 9.535878 TTGGTTAATTTGTCAGTTGGAAAATAC 57.464 29.630 0.00 0.00 0.00 1.89
6797 8973 4.069304 CCGAGGACTTGGTTAATTTGTCA 58.931 43.478 0.00 0.00 0.00 3.58
6850 9032 2.254152 TAACCAGCCTCCATCAGTCT 57.746 50.000 0.00 0.00 0.00 3.24
6851 9033 2.435805 TCATAACCAGCCTCCATCAGTC 59.564 50.000 0.00 0.00 0.00 3.51
6859 9041 3.496130 CGTCATCAATCATAACCAGCCTC 59.504 47.826 0.00 0.00 0.00 4.70
6860 9042 3.134623 TCGTCATCAATCATAACCAGCCT 59.865 43.478 0.00 0.00 0.00 4.58
6861 9043 3.466836 TCGTCATCAATCATAACCAGCC 58.533 45.455 0.00 0.00 0.00 4.85
6863 9045 6.609237 ACAATCGTCATCAATCATAACCAG 57.391 37.500 0.00 0.00 0.00 4.00
6881 9074 9.708222 CATTACTGCTGAAGTTATGTTACAATC 57.292 33.333 6.62 0.00 39.84 2.67
6981 9177 2.560105 GCAACTTTCTGGGAAAGCAGAT 59.440 45.455 16.79 2.55 0.00 2.90
7029 9225 1.672356 CCACTTCTTCCCCTGCACG 60.672 63.158 0.00 0.00 0.00 5.34
7056 9252 4.256920 CGGTGTTCCAGATCAAAGAGAAT 58.743 43.478 0.00 0.00 0.00 2.40
7143 9339 3.812053 TCTCAAGCTCTTGTTGCTTCTTC 59.188 43.478 9.20 0.00 46.39 2.87
7149 9345 2.159544 GCTGATCTCAAGCTCTTGTTGC 60.160 50.000 9.20 3.62 41.16 4.17
7189 9385 1.550976 AGGTTCAGAGGCGGAACTTAG 59.449 52.381 15.64 0.00 43.20 2.18
7191 9387 0.035458 CAGGTTCAGAGGCGGAACTT 59.965 55.000 15.64 8.48 43.20 2.66
7200 9396 0.035881 TTCTGGCAGCAGGTTCAGAG 59.964 55.000 10.34 0.00 37.52 3.35
7216 9412 7.613411 GCCCTGGCTAGATTAATTTGATATTCT 59.387 37.037 0.00 0.00 38.26 2.40
7233 9432 0.179020 CGGATGAAATGCCCTGGCTA 60.179 55.000 9.97 0.00 42.51 3.93
7267 9479 5.123502 GCAGGAAGTGATGGCATGAATATAG 59.876 44.000 3.81 0.00 0.00 1.31
7452 9664 5.641709 TGCGACTTTCTACTAAGTGATCAG 58.358 41.667 0.00 0.00 38.43 2.90
7536 10105 7.598118 GCTCTTATATTTCTTTACGGAGGGTAC 59.402 40.741 0.00 0.00 0.00 3.34
7537 10106 7.522725 CGCTCTTATATTTCTTTACGGAGGGTA 60.523 40.741 0.00 0.00 0.00 3.69
7538 10107 6.522946 GCTCTTATATTTCTTTACGGAGGGT 58.477 40.000 0.00 0.00 0.00 4.34
7539 10108 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
7540 10109 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
7541 10110 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
7542 10111 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
7543 10112 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
7555 10124 9.900710 CTACATTAGTGATCTAAACGCTCTTAT 57.099 33.333 0.00 0.00 39.23 1.73
7556 10125 8.900781 ACTACATTAGTGATCTAAACGCTCTTA 58.099 33.333 0.00 0.00 39.23 2.10
7557 10126 7.773149 ACTACATTAGTGATCTAAACGCTCTT 58.227 34.615 0.00 0.00 39.23 2.85
7558 10127 7.336161 ACTACATTAGTGATCTAAACGCTCT 57.664 36.000 0.00 0.00 39.23 4.09
7572 10141 7.336161 AGAGCGTTTAGATCACTACATTAGT 57.664 36.000 0.00 0.00 37.82 2.24
7573 10142 9.900710 ATAAGAGCGTTTAGATCACTACATTAG 57.099 33.333 0.00 0.00 37.82 1.73
7588 10157 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
7589 10158 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
7590 10159 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
7591 10160 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
7592 10161 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
7599 10168 8.639761 GCTATGTACTCCCTCTGTAAAGAAATA 58.360 37.037 0.00 0.00 0.00 1.40
7600 10169 7.125811 TGCTATGTACTCCCTCTGTAAAGAAAT 59.874 37.037 0.00 0.00 0.00 2.17
7601 10170 6.439375 TGCTATGTACTCCCTCTGTAAAGAAA 59.561 38.462 0.00 0.00 0.00 2.52
7602 10171 5.955959 TGCTATGTACTCCCTCTGTAAAGAA 59.044 40.000 0.00 0.00 0.00 2.52
7603 10172 5.516044 TGCTATGTACTCCCTCTGTAAAGA 58.484 41.667 0.00 0.00 0.00 2.52
7604 10173 5.854010 TGCTATGTACTCCCTCTGTAAAG 57.146 43.478 0.00 0.00 0.00 1.85
7605 10174 5.105064 GGTTGCTATGTACTCCCTCTGTAAA 60.105 44.000 0.00 0.00 0.00 2.01
7606 10175 4.404715 GGTTGCTATGTACTCCCTCTGTAA 59.595 45.833 0.00 0.00 0.00 2.41
7607 10176 3.958798 GGTTGCTATGTACTCCCTCTGTA 59.041 47.826 0.00 0.00 0.00 2.74
7608 10177 2.766828 GGTTGCTATGTACTCCCTCTGT 59.233 50.000 0.00 0.00 0.00 3.41
7609 10178 2.766263 TGGTTGCTATGTACTCCCTCTG 59.234 50.000 0.00 0.00 0.00 3.35
7610 10179 3.116096 TGGTTGCTATGTACTCCCTCT 57.884 47.619 0.00 0.00 0.00 3.69
7611 10180 3.451178 TCTTGGTTGCTATGTACTCCCTC 59.549 47.826 0.00 0.00 0.00 4.30
7612 10181 3.450904 TCTTGGTTGCTATGTACTCCCT 58.549 45.455 0.00 0.00 0.00 4.20
7613 10182 3.906720 TCTTGGTTGCTATGTACTCCC 57.093 47.619 0.00 0.00 0.00 4.30
7614 10183 6.073003 GCAATATCTTGGTTGCTATGTACTCC 60.073 42.308 3.07 0.00 45.41 3.85
7615 10184 6.892691 GCAATATCTTGGTTGCTATGTACTC 58.107 40.000 3.07 0.00 45.41 2.59
7616 10185 6.867662 GCAATATCTTGGTTGCTATGTACT 57.132 37.500 3.07 0.00 45.41 2.73
7687 10256 3.885484 ATGCTGAGACAAAAACGACAG 57.115 42.857 0.00 0.00 0.00 3.51
7703 10272 3.639672 TGACAGATCATCACCAATGCT 57.360 42.857 0.00 0.00 35.17 3.79
7862 10442 4.335315 CAGAACAAAACTGCAACCTCACTA 59.665 41.667 0.00 0.00 0.00 2.74
7877 10494 4.151883 AGCCTCCAAATAAGCAGAACAAA 58.848 39.130 0.00 0.00 0.00 2.83
7900 10517 0.244994 GAAGAGTCCAAGCTCGCTCA 59.755 55.000 0.00 0.00 40.26 4.26
7913 10545 2.500910 CTGCCTCTCAAGATGGAAGAGT 59.499 50.000 0.00 0.00 0.00 3.24
7914 10546 2.765135 TCTGCCTCTCAAGATGGAAGAG 59.235 50.000 3.40 0.00 30.92 2.85
7915 10547 2.825223 TCTGCCTCTCAAGATGGAAGA 58.175 47.619 3.40 3.40 33.35 2.87
7916 10548 3.842007 ATCTGCCTCTCAAGATGGAAG 57.158 47.619 0.00 0.00 0.00 3.46
7917 10549 3.520721 TCAATCTGCCTCTCAAGATGGAA 59.479 43.478 0.00 0.00 0.00 3.53
7918 10550 3.109928 TCAATCTGCCTCTCAAGATGGA 58.890 45.455 0.00 0.00 0.00 3.41
7919 10551 3.468770 CTCAATCTGCCTCTCAAGATGG 58.531 50.000 0.00 0.00 0.00 3.51
7920 10552 2.873472 GCTCAATCTGCCTCTCAAGATG 59.127 50.000 0.00 0.00 0.00 2.90
7921 10553 2.773087 AGCTCAATCTGCCTCTCAAGAT 59.227 45.455 0.00 0.00 0.00 2.40
7922 10554 2.093606 CAGCTCAATCTGCCTCTCAAGA 60.094 50.000 0.00 0.00 0.00 3.02
7923 10555 2.281517 CAGCTCAATCTGCCTCTCAAG 58.718 52.381 0.00 0.00 0.00 3.02
7924 10556 1.627329 ACAGCTCAATCTGCCTCTCAA 59.373 47.619 0.00 0.00 37.59 3.02
7925 10557 1.066358 CACAGCTCAATCTGCCTCTCA 60.066 52.381 0.00 0.00 37.59 3.27
7926 10558 1.654317 CACAGCTCAATCTGCCTCTC 58.346 55.000 0.00 0.00 37.59 3.20
7927 10559 0.392729 GCACAGCTCAATCTGCCTCT 60.393 55.000 0.00 0.00 37.59 3.69
7928 10560 1.703438 CGCACAGCTCAATCTGCCTC 61.703 60.000 0.00 0.00 37.59 4.70
7929 10561 1.744368 CGCACAGCTCAATCTGCCT 60.744 57.895 0.00 0.00 37.59 4.75
7930 10562 2.789917 CGCACAGCTCAATCTGCC 59.210 61.111 0.00 0.00 37.59 4.85
7931 10563 2.099831 GCGCACAGCTCAATCTGC 59.900 61.111 0.30 0.00 44.04 4.26
7947 10579 3.947196 TGTGATGTGATTAACCCATGAGC 59.053 43.478 0.00 0.00 0.00 4.26
7957 10589 3.354467 TGCAAGCCATGTGATGTGATTA 58.646 40.909 0.00 0.00 0.00 1.75
8003 10636 6.914215 AGCATAATTAAGCAACATGACGATTG 59.086 34.615 14.58 0.00 0.00 2.67
8051 10684 9.918630 GAGTAGTAGGTGTTTAATCACTAACAA 57.081 33.333 14.65 0.00 36.15 2.83
8061 10694 8.431910 AAGATTCAGGAGTAGTAGGTGTTTAA 57.568 34.615 0.00 0.00 0.00 1.52
8069 10702 8.948631 TGCAAATAAAGATTCAGGAGTAGTAG 57.051 34.615 0.00 0.00 0.00 2.57
8070 10703 9.905713 AATGCAAATAAAGATTCAGGAGTAGTA 57.094 29.630 0.00 0.00 0.00 1.82
8071 10704 8.680903 CAATGCAAATAAAGATTCAGGAGTAGT 58.319 33.333 0.00 0.00 0.00 2.73
8080 10713 7.322664 TCCCTGAACAATGCAAATAAAGATTC 58.677 34.615 0.00 0.00 0.00 2.52
8084 10717 5.185635 TCCTCCCTGAACAATGCAAATAAAG 59.814 40.000 0.00 0.00 0.00 1.85
8152 10788 7.201741 GCAGTCTAAAAGGATAAAAGGATCACC 60.202 40.741 0.00 0.00 0.00 4.02
8153 10789 7.336931 TGCAGTCTAAAAGGATAAAAGGATCAC 59.663 37.037 0.00 0.00 0.00 3.06
8154 10790 7.402054 TGCAGTCTAAAAGGATAAAAGGATCA 58.598 34.615 0.00 0.00 0.00 2.92
8155 10791 7.012799 CCTGCAGTCTAAAAGGATAAAAGGATC 59.987 40.741 13.81 0.00 30.92 3.36
8156 10792 6.830838 CCTGCAGTCTAAAAGGATAAAAGGAT 59.169 38.462 13.81 0.00 30.92 3.24
8157 10793 6.180472 CCTGCAGTCTAAAAGGATAAAAGGA 58.820 40.000 13.81 0.00 30.92 3.36
8158 10794 5.358160 CCCTGCAGTCTAAAAGGATAAAAGG 59.642 44.000 13.81 0.00 30.92 3.11
8159 10795 5.163612 GCCCTGCAGTCTAAAAGGATAAAAG 60.164 44.000 13.81 0.00 30.92 2.27
8160 10796 4.705023 GCCCTGCAGTCTAAAAGGATAAAA 59.295 41.667 13.81 0.00 30.92 1.52
8161 10797 4.270008 GCCCTGCAGTCTAAAAGGATAAA 58.730 43.478 13.81 0.00 30.92 1.40
8162 10798 3.371595 GGCCCTGCAGTCTAAAAGGATAA 60.372 47.826 13.81 0.00 30.92 1.75
8163 10799 2.172717 GGCCCTGCAGTCTAAAAGGATA 59.827 50.000 13.81 0.00 30.92 2.59
8164 10800 1.064389 GGCCCTGCAGTCTAAAAGGAT 60.064 52.381 13.81 0.00 30.92 3.24
8165 10801 0.328258 GGCCCTGCAGTCTAAAAGGA 59.672 55.000 13.81 0.00 30.92 3.36
8166 10802 0.038166 TGGCCCTGCAGTCTAAAAGG 59.962 55.000 13.81 5.74 0.00 3.11
8167 10803 2.019984 GATGGCCCTGCAGTCTAAAAG 58.980 52.381 13.81 0.00 0.00 2.27
8168 10804 1.354031 TGATGGCCCTGCAGTCTAAAA 59.646 47.619 13.81 0.00 0.00 1.52
8169 10805 0.991146 TGATGGCCCTGCAGTCTAAA 59.009 50.000 13.81 0.00 0.00 1.85
8170 10806 0.991146 TTGATGGCCCTGCAGTCTAA 59.009 50.000 13.81 0.00 0.00 2.10
8171 10807 0.991146 TTTGATGGCCCTGCAGTCTA 59.009 50.000 13.81 2.18 0.00 2.59
8172 10808 0.112995 TTTTGATGGCCCTGCAGTCT 59.887 50.000 13.81 0.00 0.00 3.24
8173 10809 1.188863 ATTTTGATGGCCCTGCAGTC 58.811 50.000 13.81 3.48 0.00 3.51
8174 10810 1.648116 AATTTTGATGGCCCTGCAGT 58.352 45.000 13.81 0.00 0.00 4.40
8175 10811 2.027929 TCAAATTTTGATGGCCCTGCAG 60.028 45.455 6.78 6.78 34.08 4.41
8176 10812 1.976404 TCAAATTTTGATGGCCCTGCA 59.024 42.857 7.74 0.00 34.08 4.41
8177 10813 2.766345 TCAAATTTTGATGGCCCTGC 57.234 45.000 7.74 0.00 34.08 4.85
8178 10814 6.578163 AAAATTCAAATTTTGATGGCCCTG 57.422 33.333 12.39 0.00 44.46 4.45
8200 10836 7.913297 GTGTACTTTAGCAGTTGAATGTTTCAA 59.087 33.333 0.00 0.00 46.68 2.69
8201 10837 7.414436 GTGTACTTTAGCAGTTGAATGTTTCA 58.586 34.615 0.00 0.00 36.88 2.69
8202 10838 6.856426 GGTGTACTTTAGCAGTTGAATGTTTC 59.144 38.462 0.00 0.00 36.88 2.78
8203 10839 6.320164 TGGTGTACTTTAGCAGTTGAATGTTT 59.680 34.615 0.00 0.00 36.88 2.83
8204 10840 5.825679 TGGTGTACTTTAGCAGTTGAATGTT 59.174 36.000 0.00 0.00 36.88 2.71
8205 10841 5.238650 GTGGTGTACTTTAGCAGTTGAATGT 59.761 40.000 0.00 0.00 36.88 2.71
8206 10842 5.334879 GGTGGTGTACTTTAGCAGTTGAATG 60.335 44.000 0.00 0.00 36.88 2.67
8207 10843 4.760204 GGTGGTGTACTTTAGCAGTTGAAT 59.240 41.667 0.00 0.00 36.88 2.57
8208 10844 4.131596 GGTGGTGTACTTTAGCAGTTGAA 58.868 43.478 0.00 0.00 36.88 2.69
8209 10845 3.735591 GGTGGTGTACTTTAGCAGTTGA 58.264 45.455 0.00 0.00 36.88 3.18


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

AutoCloner maintained by Alex Coulton.