Multiple sequence alignment - TraesCS2D01G486700

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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 TraesCS2D01G486700 chr2D 100.000 7069 0 0 2757 9825 586945941 586938873 0.000000e+00 13055.0
1 TraesCS2D01G486700 chr2D 100.000 2490 0 0 1 2490 586948697 586946208 0.000000e+00 4599.0
2 TraesCS2D01G486700 chr2D 78.907 659 110 23 4669 5313 332513321 332513964 4.240000e-113 420.0
3 TraesCS2D01G486700 chr2D 90.769 130 11 1 8885 9013 28724679 28724808 1.310000e-38 172.0
4 TraesCS2D01G486700 chr2D 89.552 134 13 1 9390 9522 628283369 628283502 1.700000e-37 169.0
5 TraesCS2D01G486700 chr2D 98.507 67 1 0 3550 3616 586945077 586945011 1.730000e-22 119.0
6 TraesCS2D01G486700 chr2D 98.507 67 1 0 3621 3687 586945148 586945082 1.730000e-22 119.0
7 TraesCS2D01G486700 chr2A 96.664 2878 60 5 6970 9825 721668896 721666033 0.000000e+00 4750.0
8 TraesCS2D01G486700 chr2A 95.083 2786 115 8 2759 5539 721673835 721671067 0.000000e+00 4366.0
9 TraesCS2D01G486700 chr2A 94.836 1588 63 11 892 2478 721675838 721674269 0.000000e+00 2460.0
10 TraesCS2D01G486700 chr2A 95.717 1004 35 6 5531 6529 721670174 721669174 0.000000e+00 1609.0
11 TraesCS2D01G486700 chr2A 94.384 641 20 9 14 641 721677285 721676648 0.000000e+00 970.0
12 TraesCS2D01G486700 chr2A 95.804 286 10 1 6650 6933 721669185 721668900 2.500000e-125 460.0
13 TraesCS2D01G486700 chr2A 87.970 266 4 3 630 895 721676129 721675892 1.250000e-73 289.0
14 TraesCS2D01G486700 chr2A 90.769 130 11 1 8885 9013 588083146 588083275 1.310000e-38 172.0
15 TraesCS2D01G486700 chr2A 100.000 66 0 0 3550 3615 721672979 721672914 1.340000e-23 122.0
16 TraesCS2D01G486700 chr2A 95.522 67 3 0 3621 3687 721673050 721672984 3.750000e-19 108.0
17 TraesCS2D01G486700 chr2A 92.157 51 4 0 2872 2922 554744818 554744868 1.370000e-08 73.1
18 TraesCS2D01G486700 chr2B 95.554 1372 57 2 998 2365 708547875 708549246 0.000000e+00 2193.0
19 TraesCS2D01G486700 chr2B 86.797 1795 180 29 3742 5534 708551462 708553201 0.000000e+00 1949.0
20 TraesCS2D01G486700 chr2B 91.342 1282 81 7 6968 8226 708554653 708555927 0.000000e+00 1725.0
21 TraesCS2D01G486700 chr2B 88.640 669 51 2 6279 6922 708553981 708554649 0.000000e+00 791.0
22 TraesCS2D01G486700 chr2B 93.132 364 23 2 8229 8591 708555974 708556336 5.220000e-147 532.0
23 TraesCS2D01G486700 chr2B 92.105 342 24 2 5948 6286 708553462 708553803 6.900000e-131 479.0
24 TraesCS2D01G486700 chr2B 76.923 780 141 30 4587 5343 359339196 359338433 3.300000e-109 407.0
25 TraesCS2D01G486700 chr2B 94.891 137 6 1 728 863 708547528 708547664 7.730000e-51 213.0
26 TraesCS2D01G486700 chr2B 94.545 110 6 0 889 998 708547738 708547847 4.720000e-38 171.0
27 TraesCS2D01G486700 chr2B 80.198 202 34 3 3290 3486 89450575 89450375 7.950000e-31 147.0
28 TraesCS2D01G486700 chr2B 91.429 105 8 1 2375 2478 708549309 708549413 1.030000e-29 143.0
29 TraesCS2D01G486700 chr2B 80.769 182 24 9 5979 6154 500185087 500185263 2.230000e-26 132.0
30 TraesCS2D01G486700 chr2B 87.931 116 8 4 4 113 585195835 585195720 2.230000e-26 132.0
31 TraesCS2D01G486700 chr2B 77.528 178 26 11 6078 6243 789455686 789455861 2.920000e-15 95.3
32 TraesCS2D01G486700 chr2B 94.737 38 2 0 3884 3921 648282 648245 1.070000e-04 60.2
33 TraesCS2D01G486700 chr1A 78.780 787 137 21 4574 5340 500339894 500340670 1.470000e-137 501.0
34 TraesCS2D01G486700 chr1A 77.662 385 69 15 5967 6338 375437200 375437580 1.660000e-52 219.0
35 TraesCS2D01G486700 chr1A 78.438 320 52 13 6750 7055 565020736 565021052 1.010000e-44 193.0
36 TraesCS2D01G486700 chr1A 78.438 320 52 13 6750 7055 565084916 565085232 1.010000e-44 193.0
37 TraesCS2D01G486700 chr1A 78.409 176 31 6 6060 6230 532744879 532744706 3.750000e-19 108.0
38 TraesCS2D01G486700 chr1A 97.297 37 1 0 3042 3078 251555644 251555680 8.240000e-06 63.9
39 TraesCS2D01G486700 chr5A 79.393 626 112 15 4707 5324 92447179 92447795 9.120000e-115 425.0
40 TraesCS2D01G486700 chr5A 76.913 784 145 27 4588 5358 599275188 599274428 7.100000e-111 412.0
41 TraesCS2D01G486700 chr5A 84.085 377 54 5 5559 5933 567688587 567688215 9.380000e-95 359.0
42 TraesCS2D01G486700 chr5A 80.498 482 81 12 4653 5131 27789875 27789404 3.370000e-94 357.0
43 TraesCS2D01G486700 chr5A 91.538 130 10 1 8885 9013 684323169 684323298 2.820000e-40 178.0
44 TraesCS2D01G486700 chr4B 80.952 546 84 16 4587 5120 25962002 25961465 1.970000e-111 414.0
45 TraesCS2D01G486700 chr4B 85.345 116 12 5 9279 9393 171821904 171821793 2.240000e-21 115.0
46 TraesCS2D01G486700 chr4B 80.137 146 27 2 9249 9393 642361535 642361391 3.750000e-19 108.0
47 TraesCS2D01G486700 chr4B 77.654 179 28 11 6060 6231 358476396 358476223 2.260000e-16 99.0
48 TraesCS2D01G486700 chr5B 84.856 383 52 6 5553 5933 561759523 561759145 2.000000e-101 381.0
49 TraesCS2D01G486700 chr5B 75.456 603 98 31 6506 7066 692391092 692390498 2.120000e-61 248.0
50 TraesCS2D01G486700 chr3D 78.232 611 115 18 4739 5339 421369162 421369764 9.320000e-100 375.0
51 TraesCS2D01G486700 chr3D 89.552 134 13 1 9390 9522 21895256 21895389 1.700000e-37 169.0
52 TraesCS2D01G486700 chr3D 86.325 117 13 3 1 114 584679005 584678889 3.730000e-24 124.0
53 TraesCS2D01G486700 chr3D 86.239 109 10 4 2833 2939 454759476 454759371 8.070000e-21 113.0
54 TraesCS2D01G486700 chr3D 81.416 113 17 4 2825 2935 61810573 61810463 1.360000e-13 89.8
55 TraesCS2D01G486700 chr1D 84.010 394 55 7 5553 5943 417038854 417038466 1.210000e-98 372.0
56 TraesCS2D01G486700 chr1D 89.552 134 13 1 9390 9522 254487395 254487528 1.700000e-37 169.0
57 TraesCS2D01G486700 chr1D 86.325 117 11 5 3 114 441286344 441286228 1.340000e-23 122.0
58 TraesCS2D01G486700 chr1D 84.375 128 15 4 5 130 350716060 350715936 4.820000e-23 121.0
59 TraesCS2D01G486700 chr1D 97.297 37 1 0 3042 3078 141348641 141348677 8.240000e-06 63.9
60 TraesCS2D01G486700 chr1D 97.297 37 1 0 3042 3078 350969162 350969198 8.240000e-06 63.9
61 TraesCS2D01G486700 chr6B 83.047 407 61 8 5531 5934 23741953 23742354 7.250000e-96 363.0
62 TraesCS2D01G486700 chr6B 82.547 212 31 3 3290 3496 15978188 15977978 2.180000e-41 182.0
63 TraesCS2D01G486700 chr6B 90.769 130 11 1 8885 9013 579206092 579205963 1.310000e-38 172.0
64 TraesCS2D01G486700 chr6B 89.051 137 14 1 9390 9525 579205960 579205824 1.700000e-37 169.0
65 TraesCS2D01G486700 chr6B 81.132 212 34 3 3290 3496 16024651 16024441 2.200000e-36 165.0
66 TraesCS2D01G486700 chr6B 81.132 212 34 3 3290 3496 16053141 16052931 2.200000e-36 165.0
67 TraesCS2D01G486700 chr6B 81.132 212 34 3 3290 3496 16061625 16061415 2.200000e-36 165.0
68 TraesCS2D01G486700 chr6B 74.847 326 65 13 6750 7060 143662277 143662600 2.230000e-26 132.0
69 TraesCS2D01G486700 chr6B 93.023 43 3 0 242 284 98428319 98428277 8.240000e-06 63.9
70 TraesCS2D01G486700 chr3A 83.290 389 54 10 5559 5943 23162491 23162110 2.030000e-91 348.0
71 TraesCS2D01G486700 chr3A 82.310 407 63 7 5522 5924 46571420 46571019 2.630000e-90 344.0
72 TraesCS2D01G486700 chr3A 76.253 379 66 14 6689 7048 24892530 24892157 7.840000e-41 180.0
73 TraesCS2D01G486700 chr3A 71.988 332 74 14 9078 9393 44716275 44715947 8.180000e-11 80.5
74 TraesCS2D01G486700 chr3A 77.600 125 23 5 2834 2956 51426740 51426619 4.920000e-08 71.3
75 TraesCS2D01G486700 chr4A 83.246 382 56 7 5559 5937 25136966 25137342 2.630000e-90 344.0
76 TraesCS2D01G486700 chr4A 93.617 47 2 1 2873 2918 666155403 666155449 1.770000e-07 69.4
77 TraesCS2D01G486700 chr6A 81.818 407 66 7 5531 5934 438961938 438962339 1.580000e-87 335.0
78 TraesCS2D01G486700 chr6A 90.769 130 11 1 8885 9013 592890870 592890741 1.310000e-38 172.0
79 TraesCS2D01G486700 chr6A 88.971 136 15 0 9390 9525 592890738 592890603 1.700000e-37 169.0
80 TraesCS2D01G486700 chr7A 79.891 368 65 7 4985 5343 514669493 514669126 2.720000e-65 261.0
81 TraesCS2D01G486700 chr7A 88.406 69 5 3 206 273 188868929 188868863 8.180000e-11 80.5
82 TraesCS2D01G486700 chr7A 92.500 40 1 2 4261 4299 611773240 611773202 1.000000e-03 56.5
83 TraesCS2D01G486700 chr5D 80.259 309 48 10 6767 7066 548259168 548258864 4.620000e-53 220.0
84 TraesCS2D01G486700 chr5D 90.769 130 11 1 8885 9013 6210086 6209957 1.310000e-38 172.0
85 TraesCS2D01G486700 chr5D 90.769 130 11 1 8885 9013 483797998 483797869 1.310000e-38 172.0
86 TraesCS2D01G486700 chr5D 89.051 137 14 1 9390 9525 6209954 6209818 1.700000e-37 169.0
87 TraesCS2D01G486700 chr5D 89.051 137 14 1 9390 9525 483797866 483797730 1.700000e-37 169.0
88 TraesCS2D01G486700 chr5D 82.963 135 15 5 2 130 220535998 220535866 2.240000e-21 115.0
89 TraesCS2D01G486700 chr5D 80.392 153 21 4 121 273 350382248 350382105 3.750000e-19 108.0
90 TraesCS2D01G486700 chr5D 74.153 236 47 13 6034 6259 285024455 285024686 1.760000e-12 86.1
91 TraesCS2D01G486700 chr7B 86.034 179 23 2 3742 3920 29315306 29315130 3.620000e-44 191.0
92 TraesCS2D01G486700 chr7B 87.611 113 10 4 4 112 652330550 652330438 2.880000e-25 128.0
93 TraesCS2D01G486700 chrUn 90.769 130 11 1 8885 9013 390489517 390489388 1.310000e-38 172.0
94 TraesCS2D01G486700 chrUn 89.109 101 11 0 2839 2939 49924053 49923953 1.040000e-24 126.0
95 TraesCS2D01G486700 chrUn 100.000 34 0 0 242 275 77121071 77121104 8.240000e-06 63.9
96 TraesCS2D01G486700 chrUn 97.297 37 1 0 3042 3078 246706776 246706740 8.240000e-06 63.9
97 TraesCS2D01G486700 chrUn 97.297 37 1 0 3042 3078 266191853 266191889 8.240000e-06 63.9
98 TraesCS2D01G486700 chrUn 97.297 37 1 0 3042 3078 441686791 441686755 8.240000e-06 63.9
99 TraesCS2D01G486700 chr6D 89.552 134 13 1 9390 9522 431397726 431397859 1.700000e-37 169.0
100 TraesCS2D01G486700 chr6D 97.297 37 1 0 3042 3078 430477983 430477947 8.240000e-06 63.9
101 TraesCS2D01G486700 chr7D 83.799 179 21 5 3742 3920 82274988 82274818 7.900000e-36 163.0
102 TraesCS2D01G486700 chr7D 82.105 95 15 2 2825 2918 551593328 551593421 8.180000e-11 80.5
103 TraesCS2D01G486700 chr7D 79.439 107 22 0 9287 9393 176545468 176545362 1.060000e-09 76.8
104 TraesCS2D01G486700 chr7D 84.615 65 8 2 2876 2939 84415179 84415242 8.240000e-06 63.9
105 TraesCS2D01G486700 chr3B 82.682 179 23 7 5979 6154 615384386 615384213 1.710000e-32 152.0
106 TraesCS2D01G486700 chr3B 81.564 179 22 8 5979 6154 616435539 616435369 4.790000e-28 137.0
107 TraesCS2D01G486700 chr3B 85.593 118 13 3 3 119 602330703 602330589 4.820000e-23 121.0
108 TraesCS2D01G486700 chr3B 81.188 101 8 9 6167 6259 412700379 412700476 4.920000e-08 71.3
109 TraesCS2D01G486700 chr4D 84.127 126 15 4 7 130 130169244 130169122 6.230000e-22 117.0
110 TraesCS2D01G486700 chr4D 97.297 37 1 0 3042 3078 241239834 241239870 8.240000e-06 63.9
111 TraesCS2D01G486700 chr1B 75.806 186 39 6 6079 6259 273619573 273619757 1.360000e-13 89.8


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 TraesCS2D01G486700 chr2D 586938873 586948697 9824 True 4473.000000 13055 99.253500 1 9825 4 chr2D.!!$R1 9824
1 TraesCS2D01G486700 chr2D 332513321 332513964 643 False 420.000000 420 78.907000 4669 5313 1 chr2D.!!$F2 644
2 TraesCS2D01G486700 chr2A 721666033 721677285 11252 True 1681.555556 4750 95.108889 14 9825 9 chr2A.!!$R1 9811
3 TraesCS2D01G486700 chr2B 708547528 708556336 8808 False 910.666667 2193 92.048333 728 8591 9 chr2B.!!$F3 7863
4 TraesCS2D01G486700 chr2B 359338433 359339196 763 True 407.000000 407 76.923000 4587 5343 1 chr2B.!!$R3 756
5 TraesCS2D01G486700 chr1A 500339894 500340670 776 False 501.000000 501 78.780000 4574 5340 1 chr1A.!!$F3 766
6 TraesCS2D01G486700 chr5A 92447179 92447795 616 False 425.000000 425 79.393000 4707 5324 1 chr5A.!!$F1 617
7 TraesCS2D01G486700 chr5A 599274428 599275188 760 True 412.000000 412 76.913000 4588 5358 1 chr5A.!!$R3 770
8 TraesCS2D01G486700 chr4B 25961465 25962002 537 True 414.000000 414 80.952000 4587 5120 1 chr4B.!!$R1 533
9 TraesCS2D01G486700 chr5B 692390498 692391092 594 True 248.000000 248 75.456000 6506 7066 1 chr5B.!!$R2 560
10 TraesCS2D01G486700 chr3D 421369162 421369764 602 False 375.000000 375 78.232000 4739 5339 1 chr3D.!!$F2 600

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
773 1317 0.545309 ACCAGGTGCTTCTCAGCCTA 60.545 55.000 0.00 0.00 46.74 3.93 F
1142 1797 0.254178 ATCTGCTCAACGAGGGCAAT 59.746 50.000 8.40 3.47 35.49 3.56 F
1391 2046 0.400213 GGACATCCAACTCCACCACA 59.600 55.000 0.00 0.00 35.64 4.17 F
2234 2889 1.005215 GCCTATGCCCCTGCTGATATT 59.995 52.381 0.00 0.00 38.71 1.28 F
3451 4331 0.935196 CCGTAACAATTAGAGGGCGC 59.065 55.000 0.00 0.00 0.00 6.53 F
3967 5478 1.218230 GGAATCGAGTCTGCATCCGC 61.218 60.000 13.18 0.00 39.24 5.54 F
5012 6553 0.032912 TACCGGTGCTGACCTGGATA 60.033 55.000 19.93 0.00 40.58 2.59 F
5385 6951 0.167470 CTTTGCTCACAGGTGATGCG 59.833 55.000 2.09 0.00 39.13 4.73 F
6556 9239 0.098200 TCTCAACGTGTAGCGATCCG 59.902 55.000 0.00 0.00 44.77 4.18 F
7069 9824 0.719465 CCTACATGTCGCGTGGAAAC 59.281 55.000 5.77 0.00 0.00 2.78 F
7492 10247 1.112113 GACTTAGACCATCTGGCCGA 58.888 55.000 0.00 0.00 39.32 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 2499 0.035915 GTTTCCTGCTCTCCTCCCAC 60.036 60.000 0.00 0.00 0.00 4.61 R
3083 3957 0.391661 TGCTTCAAGGAGCGGATGAC 60.392 55.000 0.00 0.00 45.64 3.06 R
3195 4069 1.170290 TCGGCAGTCGTCAGAGTCAA 61.170 55.000 0.00 0.00 40.32 3.18 R
3946 5457 0.385751 GGATGCAGACTCGATTCCGA 59.614 55.000 0.00 0.00 43.35 4.55 R
4342 5854 0.445436 GCTTCGGTTCAGATGTGCAG 59.555 55.000 0.00 0.00 0.00 4.41 R
5310 6875 2.230992 CCCATCTGTTGCATCGGAAAAA 59.769 45.455 10.27 0.00 0.00 1.94 R
6551 9234 1.296715 ACACTTGGTGAGGCGGATC 59.703 57.895 4.62 0.00 36.96 3.36 R
7217 9972 1.447317 GGGACACATATGCCGGCTTG 61.447 60.000 29.70 23.28 0.00 4.01 R
8472 11272 1.690283 CGAGCCATGAACTGCTGTCG 61.690 60.000 0.00 0.00 38.11 4.35 R
8746 11547 3.253677 AGATGCGTGCTAGAGGTATGTAC 59.746 47.826 0.00 0.00 0.00 2.90 R
9304 12105 0.324943 TTCTTGCCCTCCTACTGCAC 59.675 55.000 0.00 0.00 34.16 4.57 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
57 58 6.514012 TCTCCATGCAAGATTAAAGGGATA 57.486 37.500 0.00 0.00 0.00 2.59
60 61 8.103305 TCTCCATGCAAGATTAAAGGGATATAC 58.897 37.037 0.00 0.00 0.00 1.47
64 65 8.464404 CATGCAAGATTAAAGGGATATACCATG 58.536 37.037 6.78 0.00 41.20 3.66
79 80 7.974501 GGATATACCATGGACTAAGACATAACG 59.025 40.741 21.47 0.00 38.79 3.18
276 283 2.438021 AGCTACCACACCTTTCTCAACA 59.562 45.455 0.00 0.00 0.00 3.33
353 360 1.666553 CTTCTGTAACCGGCGCACA 60.667 57.895 10.83 3.06 0.00 4.57
423 430 5.368989 AGAAGAACTCGACAAGACCATTTT 58.631 37.500 0.00 0.00 0.00 1.82
424 431 5.823045 AGAAGAACTCGACAAGACCATTTTT 59.177 36.000 0.00 0.00 0.00 1.94
474 481 3.202906 TGAACGGGAGCAGCAATATTAC 58.797 45.455 0.00 0.00 0.00 1.89
500 507 1.143305 CAACACGCTTGTCTCAGAGG 58.857 55.000 0.00 0.00 33.55 3.69
584 592 1.588404 CGACGGTGCACTGATATGTTC 59.412 52.381 31.98 16.14 0.00 3.18
586 594 3.262420 GACGGTGCACTGATATGTTCTT 58.738 45.455 31.98 5.98 0.00 2.52
662 1206 0.804989 CTGCCGACAATGAACCTTCC 59.195 55.000 0.00 0.00 0.00 3.46
773 1317 0.545309 ACCAGGTGCTTCTCAGCCTA 60.545 55.000 0.00 0.00 46.74 3.93
778 1322 1.082690 GTGCTTCTCAGCCTAGTTGC 58.917 55.000 0.00 0.00 46.74 4.17
869 1413 9.734984 ATTAAGATTAGTGTTTATATTCCCCCG 57.265 33.333 0.00 0.00 0.00 5.73
870 1414 5.557866 AGATTAGTGTTTATATTCCCCCGC 58.442 41.667 0.00 0.00 0.00 6.13
871 1415 4.774660 TTAGTGTTTATATTCCCCCGCA 57.225 40.909 0.00 0.00 0.00 5.69
1014 1666 1.750682 GCCCCTATCTTTGCCGTCAAT 60.751 52.381 0.00 0.00 31.33 2.57
1141 1796 0.391661 GATCTGCTCAACGAGGGCAA 60.392 55.000 8.40 1.54 35.49 4.52
1142 1797 0.254178 ATCTGCTCAACGAGGGCAAT 59.746 50.000 8.40 3.47 35.49 3.56
1234 1889 1.549170 GTCCACCAACAGATACCTCGT 59.451 52.381 0.00 0.00 0.00 4.18
1293 1948 3.419759 CGAACCGTGAAAGGCCCG 61.420 66.667 0.00 0.00 33.69 6.13
1391 2046 0.400213 GGACATCCAACTCCACCACA 59.600 55.000 0.00 0.00 35.64 4.17
1404 2059 2.360852 CCACAAGGGCAGCTCCTG 60.361 66.667 3.39 0.00 37.20 3.86
1612 2267 1.996786 TATCGGTTCGTCACGGAGGC 61.997 60.000 0.00 0.00 38.08 4.70
1655 2310 3.612247 CTGGGACGGGAGCACCAAG 62.612 68.421 1.58 0.00 38.28 3.61
1722 2377 3.989566 GAGGACGCGACGTACACCG 62.990 68.421 15.93 0.00 44.03 4.94
1844 2499 1.283793 CTTTGTCAAGCGGCTGGTG 59.716 57.895 1.81 0.00 0.00 4.17
1858 2513 1.897225 CTGGTGTGGGAGGAGAGCAG 61.897 65.000 0.00 0.00 0.00 4.24
1860 2515 1.610673 GTGTGGGAGGAGAGCAGGA 60.611 63.158 0.00 0.00 0.00 3.86
1988 2643 3.612247 CTGTCCCAGGGGCTTCACG 62.612 68.421 12.68 0.00 34.68 4.35
2186 2841 3.640407 GTGGAGGAGTGCAGGGCA 61.640 66.667 0.00 0.00 35.60 5.36
2211 2866 3.182590 TTCGCCAACTGCTCCTGCT 62.183 57.895 0.00 0.00 40.48 4.24
2234 2889 1.005215 GCCTATGCCCCTGCTGATATT 59.995 52.381 0.00 0.00 38.71 1.28
2398 3108 8.121167 TCACCGAAAACAACAATTTCAATTAC 57.879 30.769 0.00 0.00 36.75 1.89
2829 3703 2.239400 CGGGCAGATAGTCCATCACTA 58.761 52.381 0.00 0.00 44.49 2.74
2918 3792 1.703411 CCACATATCCGGCCCAAATT 58.297 50.000 0.00 0.00 0.00 1.82
2943 3817 4.348486 GAGTAGATATGAGGAGGCATGGA 58.652 47.826 0.00 0.00 0.00 3.41
2997 3871 1.285573 CCACCCCCATCCCACATACA 61.286 60.000 0.00 0.00 0.00 2.29
3013 3887 6.089476 CCACATACATAGAAGTAGATGAGCG 58.911 44.000 0.00 0.00 0.00 5.03
3083 3957 5.474532 TCCAACTCAATGTCAAGGATCTTTG 59.525 40.000 11.18 11.18 0.00 2.77
3195 4069 2.440796 CATGCCGGGCAGTGGATT 60.441 61.111 27.62 6.26 43.65 3.01
3247 4121 4.408821 GTCCTCCCATGCGTGCCA 62.409 66.667 0.00 0.00 0.00 4.92
3306 4180 1.792006 GTCCGACCGATGTTGAAGTT 58.208 50.000 0.00 0.00 0.00 2.66
3315 4189 3.559655 CCGATGTTGAAGTTTGTCTGTCA 59.440 43.478 0.00 0.00 0.00 3.58
3340 4214 1.440850 CATTGTGACGGCGCAACTG 60.441 57.895 21.53 15.04 46.22 3.16
3416 4294 4.296690 GTCTGCCGGTATATGAGTGTTAC 58.703 47.826 1.90 0.00 0.00 2.50
3451 4331 0.935196 CCGTAACAATTAGAGGGCGC 59.065 55.000 0.00 0.00 0.00 6.53
3575 4455 4.643387 ACACTCGTGCCCTTGCCC 62.643 66.667 0.00 0.00 36.33 5.36
3682 4562 1.304282 GTCCATGCCATGACTGGGT 59.696 57.895 6.18 0.00 43.36 4.51
3686 4566 1.683365 ATGCCATGACTGGGTTGCC 60.683 57.895 0.00 0.00 43.36 4.52
3715 4595 3.870633 ACTAGTTTAGTTGGGCTCTCG 57.129 47.619 0.00 0.00 34.86 4.04
3946 5457 4.814294 GTTCCGAGGTCGCGCCAT 62.814 66.667 19.30 0.00 40.61 4.40
3967 5478 1.218230 GGAATCGAGTCTGCATCCGC 61.218 60.000 13.18 0.00 39.24 5.54
4061 5573 2.050351 CGTCGTCTGTCGTGGCTT 60.050 61.111 0.00 0.00 40.80 4.35
4221 5733 2.437359 AGCATCGAGTGGCCTTGC 60.437 61.111 3.32 3.81 0.00 4.01
4267 5779 1.551329 GGCCAGGGACCCAATTGTTAA 60.551 52.381 14.60 0.00 0.00 2.01
4315 5827 5.076182 TGTGCTATTTTTCAAGGACCATGA 58.924 37.500 0.00 0.00 33.53 3.07
4342 5854 6.510879 AAATTTAGCTACTAACAAGTGGGC 57.489 37.500 0.00 0.00 0.00 5.36
4356 5868 1.303561 TGGGCTGCACATCTGAACC 60.304 57.895 0.00 0.00 0.00 3.62
4489 6001 7.225538 GCTAGAGTTGCTCTTAATCTAAATGCA 59.774 37.037 3.87 0.00 41.50 3.96
4515 6027 9.541884 ACTTCTCTTCTATTACCTCTTCTCTTT 57.458 33.333 0.00 0.00 0.00 2.52
4864 6401 7.883391 TCCAAACTCCAACAACTTTAACATA 57.117 32.000 0.00 0.00 0.00 2.29
5002 6543 3.869246 CGTATTTCTTTCATACCGGTGCT 59.131 43.478 19.93 0.46 0.00 4.40
5012 6553 0.032912 TACCGGTGCTGACCTGGATA 60.033 55.000 19.93 0.00 40.58 2.59
5148 6706 4.499183 AGAGACGCCTTAAGATTGACAAG 58.501 43.478 3.36 0.00 0.00 3.16
5310 6875 5.342866 AGGTTAGGAGAGTGTGGTATTCTT 58.657 41.667 0.00 0.00 0.00 2.52
5385 6951 0.167470 CTTTGCTCACAGGTGATGCG 59.833 55.000 2.09 0.00 39.13 4.73
5569 8039 6.073765 ACACACAAGATTGACTATTTCGTCAC 60.074 38.462 0.00 0.00 43.11 3.67
5570 8040 5.408604 ACACAAGATTGACTATTTCGTCACC 59.591 40.000 0.00 0.00 43.11 4.02
5577 8047 1.553704 ACTATTTCGTCACCCTGGGTC 59.446 52.381 17.46 4.76 31.02 4.46
5597 8067 7.060421 TGGGTCAGGAATAATTATTCTTCACC 58.940 38.462 25.83 25.83 41.33 4.02
5598 8068 6.490381 GGGTCAGGAATAATTATTCTTCACCC 59.510 42.308 32.45 32.45 41.56 4.61
5636 8106 6.751425 ACATGAATGCACCATAATTTTACGTG 59.249 34.615 0.00 0.00 0.00 4.49
5637 8107 6.260870 TGAATGCACCATAATTTTACGTGT 57.739 33.333 0.00 0.00 0.00 4.49
5638 8108 6.682746 TGAATGCACCATAATTTTACGTGTT 58.317 32.000 0.00 0.00 0.00 3.32
5639 8109 7.817641 TGAATGCACCATAATTTTACGTGTTA 58.182 30.769 0.00 0.00 0.00 2.41
5645 8115 9.557338 GCACCATAATTTTACGTGTTATGTAAA 57.443 29.630 0.00 3.03 37.68 2.01
5787 8258 9.875708 ATACAATTTTTATGGGCTTATGACCTA 57.124 29.630 1.59 0.00 43.49 3.08
5916 8388 5.363939 GGTGAAGAGTAGCTTATTCTGCAT 58.636 41.667 0.00 0.00 33.30 3.96
5922 8394 4.701765 AGTAGCTTATTCTGCATCCTGTG 58.298 43.478 0.00 0.00 0.00 3.66
6249 8724 6.646267 TGACTGTAGACAAACCTAAAACACT 58.354 36.000 0.00 0.00 0.00 3.55
6259 8734 8.975410 ACAAACCTAAAACACTGAGTAAAAAC 57.025 30.769 0.00 0.00 0.00 2.43
6466 9147 7.284944 TCAATGGAGAAATGCCAAAAATTTGTT 59.715 29.630 5.27 0.00 39.21 2.83
6471 9152 5.299028 AGAAATGCCAAAAATTTGTTGTCCC 59.701 36.000 5.27 0.00 36.45 4.46
6473 9154 4.162040 TGCCAAAAATTTGTTGTCCCAT 57.838 36.364 5.27 0.00 36.45 4.00
6532 9213 9.658799 TCTTCAAAAGTTCATCTCCACTATAAG 57.341 33.333 0.00 0.00 0.00 1.73
6544 9227 6.042777 TCTCCACTATAAGCAATTCTCAACG 58.957 40.000 0.00 0.00 0.00 4.10
6547 9230 5.351465 CCACTATAAGCAATTCTCAACGTGT 59.649 40.000 0.00 0.00 0.00 4.49
6556 9239 0.098200 TCTCAACGTGTAGCGATCCG 59.902 55.000 0.00 0.00 44.77 4.18
6577 9260 1.321474 CTCACCAAGTGTGCCATGTT 58.679 50.000 0.00 0.00 45.03 2.71
6578 9261 1.267806 CTCACCAAGTGTGCCATGTTC 59.732 52.381 0.00 0.00 45.03 3.18
6641 9324 8.902806 TCCATGACATTTAATTCCTACAACATC 58.097 33.333 0.00 0.00 0.00 3.06
6684 9376 3.938653 GCATGTCTGCCACATCATG 57.061 52.632 0.00 0.00 44.60 3.07
7069 9824 0.719465 CCTACATGTCGCGTGGAAAC 59.281 55.000 5.77 0.00 0.00 2.78
7217 9972 1.545841 AGCCACGGAAGAATTTTCCC 58.454 50.000 11.45 0.00 35.17 3.97
7327 10082 2.287668 CGGATTTGGCGTGGTTTACAAA 60.288 45.455 0.00 0.00 37.25 2.83
7421 10176 6.767524 TGTTGGTTGACTTGACTGTATTTT 57.232 33.333 0.00 0.00 0.00 1.82
7492 10247 1.112113 GACTTAGACCATCTGGCCGA 58.888 55.000 0.00 0.00 39.32 5.54
8101 10857 3.244249 GGGGATACATTGCTCCAGAGTAC 60.244 52.174 7.85 0.00 39.74 2.73
8472 11272 2.167900 AGAGGTGGTCGTAATGCTAACC 59.832 50.000 0.00 0.00 0.00 2.85
8631 11431 3.310307 GCACCCCGGGCAAACATT 61.310 61.111 17.73 0.00 0.00 2.71
8765 11566 2.357952 CTGTACATACCTCTAGCACGCA 59.642 50.000 0.00 0.00 0.00 5.24
8875 11676 6.366630 GGAAATGATATCTAGCGAACTTTGC 58.633 40.000 3.98 0.00 0.00 3.68
8937 11738 4.279420 GGCCTTTTGTTCTTCTTCACATCT 59.721 41.667 0.00 0.00 0.00 2.90
8938 11739 5.218139 GCCTTTTGTTCTTCTTCACATCTG 58.782 41.667 0.00 0.00 0.00 2.90
8951 11752 6.446318 TCTTCACATCTGTTATTTTTGCACC 58.554 36.000 0.00 0.00 0.00 5.01
9019 11820 7.022055 TGTACGAAATGAATCTCTCTCTCTC 57.978 40.000 0.00 0.00 0.00 3.20
9020 11821 6.826231 TGTACGAAATGAATCTCTCTCTCTCT 59.174 38.462 0.00 0.00 0.00 3.10
9021 11822 6.377327 ACGAAATGAATCTCTCTCTCTCTC 57.623 41.667 0.00 0.00 0.00 3.20
9022 11823 6.122277 ACGAAATGAATCTCTCTCTCTCTCT 58.878 40.000 0.00 0.00 0.00 3.10
9023 11824 6.260936 ACGAAATGAATCTCTCTCTCTCTCTC 59.739 42.308 0.00 0.00 0.00 3.20
9024 11825 6.484643 CGAAATGAATCTCTCTCTCTCTCTCT 59.515 42.308 0.00 0.00 0.00 3.10
9025 11826 7.307632 CGAAATGAATCTCTCTCTCTCTCTCTC 60.308 44.444 0.00 0.00 0.00 3.20
9026 11827 6.760440 ATGAATCTCTCTCTCTCTCTCTCT 57.240 41.667 0.00 0.00 0.00 3.10
9027 11828 6.166984 TGAATCTCTCTCTCTCTCTCTCTC 57.833 45.833 0.00 0.00 0.00 3.20
9028 11829 5.901853 TGAATCTCTCTCTCTCTCTCTCTCT 59.098 44.000 0.00 0.00 0.00 3.10
9029 11830 6.041409 TGAATCTCTCTCTCTCTCTCTCTCTC 59.959 46.154 0.00 0.00 0.00 3.20
9030 11831 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
9031 11832 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
9032 11833 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
9057 11858 5.523588 TCTCTCTCTCTCTCTCTCTCTCTT 58.476 45.833 0.00 0.00 0.00 2.85
9068 11869 8.548025 TCTCTCTCTCTCTCTTTCTCTCAATAA 58.452 37.037 0.00 0.00 0.00 1.40
9139 11940 2.808543 CAAGCACCCACACTAAGAAGAC 59.191 50.000 0.00 0.00 0.00 3.01
9146 11947 2.300152 CCACACTAAGAAGACTGCTGGA 59.700 50.000 0.00 0.00 0.00 3.86
9175 11976 0.597568 CAATCGTGCCCAAGAAGCAA 59.402 50.000 0.00 0.00 43.02 3.91
9224 12025 2.159627 GTGTCAACCTAACAAGCATCCG 59.840 50.000 0.00 0.00 0.00 4.18
9300 12101 1.153549 GACTCCTAGCAAGCGGGTG 60.154 63.158 6.91 7.12 0.00 4.61
9304 12105 1.448540 CCTAGCAAGCGGGTGTCAG 60.449 63.158 0.00 0.00 0.00 3.51
9310 12111 3.106986 AAGCGGGTGTCAGTGCAGT 62.107 57.895 0.00 0.00 0.00 4.40
9337 12138 6.405176 GGAGGGCAAGAAATTTGAAGTATGAG 60.405 42.308 0.00 0.00 0.00 2.90
9341 12142 7.370383 GGCAAGAAATTTGAAGTATGAGTCAA 58.630 34.615 0.00 0.00 31.99 3.18
9353 12154 2.203337 AGTCAAAAGCCTGCCGCA 60.203 55.556 0.00 0.00 41.38 5.69
9363 12164 0.819259 GCCTGCCGCAGAAATATCCA 60.819 55.000 22.35 0.00 37.47 3.41
9375 12176 5.533903 GCAGAAATATCCACTCAATCACCAT 59.466 40.000 0.00 0.00 0.00 3.55
9395 12196 4.574828 CCATTTTATTGTGAGTAGTCCCCG 59.425 45.833 0.00 0.00 0.00 5.73
9550 12351 5.231702 TGATGTGAGAAAAATTGCCACATG 58.768 37.500 10.50 0.00 45.20 3.21
9572 12373 2.260481 CGGTTTTAGGAGAGTTCGCTC 58.740 52.381 0.00 0.00 44.41 5.03
9621 12422 1.166531 GCTCACCTTGTCCACCACAC 61.167 60.000 0.00 0.00 33.41 3.82
9622 12423 0.535102 CTCACCTTGTCCACCACACC 60.535 60.000 0.00 0.00 33.41 4.16
9691 12492 0.700564 ACTCCATCACACCCATTGCT 59.299 50.000 0.00 0.00 0.00 3.91
9702 12503 3.257561 CATTGCTCGTCGGCTCCG 61.258 66.667 1.14 1.14 41.35 4.63
9768 12569 1.135431 CAGTGTCAGAGCTCGAAGGAG 60.135 57.143 8.37 0.00 43.46 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.842531 TCTTGCATGGAGATTCCTACAA 57.157 40.909 0.00 0.00 36.69 2.41
30 31 5.010415 CCCTTTAATCTTGCATGGAGATTCC 59.990 44.000 13.99 0.00 41.59 3.01
57 58 6.971726 TCGTTATGTCTTAGTCCATGGTAT 57.028 37.500 12.58 4.07 0.00 2.73
60 61 5.661458 ACTTCGTTATGTCTTAGTCCATGG 58.339 41.667 4.97 4.97 0.00 3.66
64 65 6.192234 TGAGACTTCGTTATGTCTTAGTCC 57.808 41.667 0.00 0.00 42.79 3.85
252 259 0.984995 AGAAAGGTGTGGTAGCTCCC 59.015 55.000 0.00 0.00 35.72 4.30
276 283 3.181478 ACAGAAGACCGAGACGTTTTCTT 60.181 43.478 0.00 0.00 33.22 2.52
353 360 2.614057 CGTTGACAAGTTCTTTCCTGCT 59.386 45.455 0.00 0.00 0.00 4.24
424 431 5.492895 TCAGATACGCCCATTACTGAAAAA 58.507 37.500 0.00 0.00 32.66 1.94
425 432 5.092554 TCAGATACGCCCATTACTGAAAA 57.907 39.130 0.00 0.00 32.66 2.29
434 441 2.700371 TCAACAGATCAGATACGCCCAT 59.300 45.455 0.00 0.00 0.00 4.00
500 507 4.142315 TGACCTACCTACTGACGTAATTGC 60.142 45.833 0.00 0.00 0.00 3.56
565 572 2.893637 AGAACATATCAGTGCACCGTC 58.106 47.619 14.63 0.00 0.00 4.79
586 594 4.688021 AGCGATACAAAAACAGGCAAAAA 58.312 34.783 0.00 0.00 0.00 1.94
591 599 2.595386 CCAAGCGATACAAAAACAGGC 58.405 47.619 0.00 0.00 0.00 4.85
592 600 2.595386 GCCAAGCGATACAAAAACAGG 58.405 47.619 0.00 0.00 0.00 4.00
593 601 2.595386 GGCCAAGCGATACAAAAACAG 58.405 47.619 0.00 0.00 0.00 3.16
595 603 1.271102 TGGGCCAAGCGATACAAAAAC 59.729 47.619 2.13 0.00 0.00 2.43
596 604 1.543802 CTGGGCCAAGCGATACAAAAA 59.456 47.619 8.04 0.00 0.00 1.94
597 605 1.173043 CTGGGCCAAGCGATACAAAA 58.827 50.000 8.04 0.00 0.00 2.44
598 606 0.679640 CCTGGGCCAAGCGATACAAA 60.680 55.000 8.04 0.00 0.00 2.83
599 607 1.077787 CCTGGGCCAAGCGATACAA 60.078 57.895 8.04 0.00 0.00 2.41
662 1206 0.815095 TGCATCTTCAATGCTGCCAG 59.185 50.000 10.96 0.00 44.79 4.85
773 1317 1.878953 CTACAACTCAACCGGCAACT 58.121 50.000 0.00 0.00 0.00 3.16
778 1322 1.808411 ACATGCTACAACTCAACCGG 58.192 50.000 0.00 0.00 0.00 5.28
988 1612 2.456577 GGCAAAGATAGGGGCTTTTCA 58.543 47.619 0.00 0.00 33.56 2.69
989 1613 1.405463 CGGCAAAGATAGGGGCTTTTC 59.595 52.381 0.00 0.00 33.56 2.29
1014 1666 6.317140 ACTTCCATTACGACTTACGAGTATGA 59.683 38.462 0.00 0.00 45.77 2.15
1141 1796 1.338294 TGTTGCCGTCGGTGATGTTAT 60.338 47.619 13.94 0.00 0.00 1.89
1142 1797 0.033642 TGTTGCCGTCGGTGATGTTA 59.966 50.000 13.94 0.00 0.00 2.41
1234 1889 2.462723 TGGACACGGAGAACCATATCA 58.537 47.619 0.00 0.00 35.59 2.15
1404 2059 2.985847 AAGAAGCTGCGCAACCCC 60.986 61.111 13.05 1.28 0.00 4.95
1478 2133 3.483922 GCGTGTCAGACAGATAATCGAAG 59.516 47.826 2.53 0.00 0.00 3.79
1655 2310 4.468689 GGCCCTGTGCGGTAGACC 62.469 72.222 0.00 0.00 42.61 3.85
1714 2369 2.400399 ACTTGAACATGTCGGTGTACG 58.600 47.619 0.00 0.00 46.11 3.67
1715 2370 3.121126 CGAACTTGAACATGTCGGTGTAC 60.121 47.826 0.00 0.00 0.00 2.90
1722 2377 2.792674 TGACGACGAACTTGAACATGTC 59.207 45.455 0.00 0.00 0.00 3.06
1844 2499 0.035915 GTTTCCTGCTCTCCTCCCAC 60.036 60.000 0.00 0.00 0.00 4.61
1852 2507 0.539051 CTCCCATCGTTTCCTGCTCT 59.461 55.000 0.00 0.00 0.00 4.09
1858 2513 1.555533 AGAAGGTCTCCCATCGTTTCC 59.444 52.381 0.00 0.00 33.59 3.13
1860 2515 2.876079 GCAAGAAGGTCTCCCATCGTTT 60.876 50.000 0.00 0.00 33.59 3.60
2398 3108 6.463360 AGCAAAATTATTTAACCACCCACTG 58.537 36.000 0.00 0.00 0.00 3.66
2756 3495 1.818674 GGTCGGATTTGGCTTGTCAAT 59.181 47.619 0.00 0.00 0.00 2.57
2757 3496 1.243902 GGTCGGATTTGGCTTGTCAA 58.756 50.000 0.00 0.00 0.00 3.18
2918 3792 4.199002 TGCCTCCTCATATCTACTCCAA 57.801 45.455 0.00 0.00 0.00 3.53
2997 3871 5.825679 ACTTCACTCGCTCATCTACTTCTAT 59.174 40.000 0.00 0.00 0.00 1.98
3013 3887 4.732672 ACGGGGTTATCTAACTTCACTC 57.267 45.455 0.52 0.00 36.47 3.51
3083 3957 0.391661 TGCTTCAAGGAGCGGATGAC 60.392 55.000 0.00 0.00 45.64 3.06
3152 4026 2.438763 AGAGGGCCAGAAATCATCAGAG 59.561 50.000 6.18 0.00 0.00 3.35
3195 4069 1.170290 TCGGCAGTCGTCAGAGTCAA 61.170 55.000 0.00 0.00 40.32 3.18
3306 4180 3.064682 CACAATGGTTTCGTGACAGACAA 59.935 43.478 0.00 0.00 32.23 3.18
3315 4189 1.837538 CGCCGTCACAATGGTTTCGT 61.838 55.000 0.00 0.00 33.68 3.85
3356 4230 2.125350 CCTCGAGCTTCCAGCACC 60.125 66.667 6.99 0.00 45.56 5.01
3416 4294 2.398554 CGGCGAACACCAATCCCTG 61.399 63.158 0.00 0.00 0.00 4.45
3682 4562 7.708752 CCAACTAAACTAGTTTCATTTTGGCAA 59.291 33.333 23.76 0.00 46.27 4.52
3686 4566 7.433680 AGCCCAACTAAACTAGTTTCATTTTG 58.566 34.615 23.76 19.29 46.27 2.44
3710 4590 2.032302 CGAGTGTTCCCTGATACGAGAG 59.968 54.545 0.00 0.00 0.00 3.20
3715 4595 1.641577 GCACGAGTGTTCCCTGATAC 58.358 55.000 5.07 0.00 0.00 2.24
3945 5456 1.000283 GGATGCAGACTCGATTCCGAT 60.000 52.381 0.00 0.00 44.62 4.18
3946 5457 0.385751 GGATGCAGACTCGATTCCGA 59.614 55.000 0.00 0.00 43.35 4.55
4201 5713 0.674581 CAAGGCCACTCGATGCTCAA 60.675 55.000 5.01 0.00 0.00 3.02
4267 5779 3.944650 GCACCCTCAAAACAAAAACCAAT 59.055 39.130 0.00 0.00 0.00 3.16
4315 5827 9.174166 CCCACTTGTTAGTAGCTAAATTTACAT 57.826 33.333 0.00 0.00 31.96 2.29
4342 5854 0.445436 GCTTCGGTTCAGATGTGCAG 59.555 55.000 0.00 0.00 0.00 4.41
4356 5868 6.017605 AGAGCAGATACCATAAAATTGCTTCG 60.018 38.462 0.00 0.00 40.19 3.79
4489 6001 9.541884 AAAGAGAAGAGGTAATAGAAGAGAAGT 57.458 33.333 0.00 0.00 0.00 3.01
4694 6212 4.821805 TCAGAAACATCACAGGGTTTTCTC 59.178 41.667 0.00 0.00 37.35 2.87
4941 6480 3.739401 AAGGTTGCACCCTAAATAGCT 57.261 42.857 1.94 0.00 39.75 3.32
5002 6543 6.382859 TGCTAGTATGTTTTCTATCCAGGTCA 59.617 38.462 0.00 0.00 0.00 4.02
5012 6553 9.740710 AATCCTAGTTTTGCTAGTATGTTTTCT 57.259 29.630 0.00 0.00 44.37 2.52
5148 6706 9.478019 CTCACACAATTAGAACGTATTTGAATC 57.522 33.333 0.00 0.00 0.00 2.52
5310 6875 2.230992 CCCATCTGTTGCATCGGAAAAA 59.769 45.455 10.27 0.00 0.00 1.94
5385 6951 4.539870 CATATGGAAACGAATGATGTGGC 58.460 43.478 0.00 0.00 0.00 5.01
5539 7105 9.516314 CGAAATAGTCAATCTTGTGTGTCTATA 57.484 33.333 0.00 0.00 0.00 1.31
5542 7108 6.223852 ACGAAATAGTCAATCTTGTGTGTCT 58.776 36.000 0.00 0.00 0.00 3.41
5543 7109 6.145534 TGACGAAATAGTCAATCTTGTGTGTC 59.854 38.462 0.00 0.00 46.81 3.67
5544 7110 5.989168 TGACGAAATAGTCAATCTTGTGTGT 59.011 36.000 0.00 0.00 46.81 3.72
5577 8047 6.901081 GGGGGTGAAGAATAATTATTCCTG 57.099 41.667 27.18 0.00 42.29 3.86
5597 8067 4.038402 GCATTCATGTGAAAATAGAGGGGG 59.962 45.833 0.00 0.00 37.61 5.40
5598 8068 4.646040 TGCATTCATGTGAAAATAGAGGGG 59.354 41.667 0.00 0.00 37.61 4.79
5769 8240 9.739276 CAGAAATATAGGTCATAAGCCCATAAA 57.261 33.333 0.00 0.00 0.00 1.40
5774 8245 8.465273 AAAACAGAAATATAGGTCATAAGCCC 57.535 34.615 0.00 0.00 0.00 5.19
5874 8345 7.507956 TCTTCACCCGAGGTAATCTTATGATTA 59.492 37.037 6.91 6.91 42.37 1.75
5889 8360 4.339814 AGAATAAGCTACTCTTCACCCGAG 59.660 45.833 0.00 0.00 36.25 4.63
5916 8388 6.550938 AGATTGACTATTCATCACACAGGA 57.449 37.500 0.00 0.00 0.00 3.86
5922 8394 9.197694 GGTGTGTATAGATTGACTATTCATCAC 57.802 37.037 1.99 1.99 39.66 3.06
6249 8724 8.836268 ATACTCCGTATGTTTGTTTTTACTCA 57.164 30.769 0.00 0.00 0.00 3.41
6259 8734 9.745880 AGTGTTCTTATATACTCCGTATGTTTG 57.254 33.333 0.00 0.00 30.79 2.93
6471 9152 4.493872 CCCGTGCAAAAGACAAAACAAATG 60.494 41.667 0.00 0.00 0.00 2.32
6473 9154 2.996621 CCCGTGCAAAAGACAAAACAAA 59.003 40.909 0.00 0.00 0.00 2.83
6532 9213 1.724623 TCGCTACACGTTGAGAATTGC 59.275 47.619 0.00 0.00 44.19 3.56
6551 9234 1.296715 ACACTTGGTGAGGCGGATC 59.703 57.895 4.62 0.00 36.96 3.36
6577 9260 3.819564 AAATAGTGCTAGTGGATGCGA 57.180 42.857 0.00 0.00 0.00 5.10
6578 9261 4.332543 TCAAAAATAGTGCTAGTGGATGCG 59.667 41.667 0.00 0.00 0.00 4.73
6641 9324 2.830923 ACTTGGTGAGATGAGAGAGTGG 59.169 50.000 0.00 0.00 0.00 4.00
6813 9537 2.231721 TGGACGACACACCATCGAATAA 59.768 45.455 0.78 0.00 42.25 1.40
7217 9972 1.447317 GGGACACATATGCCGGCTTG 61.447 60.000 29.70 23.28 0.00 4.01
7492 10247 3.636764 AGTCATTCTTGCCTTTTTCCGTT 59.363 39.130 0.00 0.00 0.00 4.44
7529 10284 2.494059 CGTGACCCTTGACATCACTTT 58.506 47.619 5.60 0.00 40.51 2.66
8009 10765 9.797642 AGAAAAATAAGGGAGCATTTGAAATTT 57.202 25.926 0.00 0.00 0.00 1.82
8101 10857 2.282462 AGGTTGCCTTCCCTTGCG 60.282 61.111 0.00 0.00 0.00 4.85
8472 11272 1.690283 CGAGCCATGAACTGCTGTCG 61.690 60.000 0.00 0.00 38.11 4.35
8631 11431 7.432350 AAAATCACAAAAACTTGTTCTTGCA 57.568 28.000 0.09 0.00 31.86 4.08
8664 11465 7.122353 ACAAGAATTCAATCTGAAAGGATCCAG 59.878 37.037 15.82 2.06 40.12 3.86
8746 11547 3.253677 AGATGCGTGCTAGAGGTATGTAC 59.746 47.826 0.00 0.00 0.00 2.90
9019 11820 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
9020 11821 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
9021 11822 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
9022 11823 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
9023 11824 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
9024 11825 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
9025 11826 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
9026 11827 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
9027 11828 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
9028 11829 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
9029 11830 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
9030 11831 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
9031 11832 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
9032 11833 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
9159 11960 1.107114 TTTTTGCTTCTTGGGCACGA 58.893 45.000 0.00 0.00 39.55 4.35
9175 11976 6.371548 GGTGGCTTTGTTTTCTCTTTCTTTTT 59.628 34.615 0.00 0.00 0.00 1.94
9224 12025 2.968330 CTAGCTGCTCCGCGACGTAC 62.968 65.000 8.23 0.00 34.40 3.67
9245 12046 2.666190 GCTTCTGCTGGACGCACA 60.666 61.111 4.47 0.00 45.47 4.57
9300 12101 1.219393 GCCCTCCTACTGCACTGAC 59.781 63.158 0.00 0.00 0.00 3.51
9304 12105 0.324943 TTCTTGCCCTCCTACTGCAC 59.675 55.000 0.00 0.00 34.16 4.57
9310 12111 4.998051 ACTTCAAATTTCTTGCCCTCCTA 58.002 39.130 0.00 0.00 0.00 2.94
9337 12138 1.795170 TTCTGCGGCAGGCTTTTGAC 61.795 55.000 28.18 0.00 44.05 3.18
9341 12142 1.678101 GATATTTCTGCGGCAGGCTTT 59.322 47.619 28.18 13.92 44.05 3.51
9353 12154 8.599624 AAAATGGTGATTGAGTGGATATTTCT 57.400 30.769 0.00 0.00 0.00 2.52
9363 12164 7.765695 ACTCACAATAAAATGGTGATTGAGT 57.234 32.000 0.00 0.00 40.44 3.41
9375 12176 4.895668 ACGGGGACTACTCACAATAAAA 57.104 40.909 0.00 0.00 0.00 1.52
9480 12281 7.893658 TGGTAAACCAAAAACAGTCTAAACAA 58.106 30.769 0.00 0.00 44.35 2.83
9550 12351 1.991264 GCGAACTCTCCTAAAACCGTC 59.009 52.381 0.00 0.00 0.00 4.79
9572 12373 0.937699 TTCGCACTCGAGTTGTTCCG 60.938 55.000 17.26 13.25 46.34 4.30
9592 12393 3.288308 AAGGTGAGCGAGTGAGCCG 62.288 63.158 0.00 0.00 38.01 5.52
9621 12422 1.984026 GGTGGGGAATTGTGGCAGG 60.984 63.158 0.00 0.00 0.00 4.85
9622 12423 1.984026 GGGTGGGGAATTGTGGCAG 60.984 63.158 0.00 0.00 0.00 4.85
9768 12569 2.887568 CACCTCCATCAGCGTCGC 60.888 66.667 9.80 9.80 0.00 5.19


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

AutoCloner maintained by Alex Coulton.