Multiple sequence alignment - TraesCS5D01G123500

Loading Multiple Alignment...

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 TraesCS5D01G123500 chr5D 100.000 4499 0 0 1 4499 181890303 181885805 0.000000e+00 8309.0
1 TraesCS5D01G123500 chr5D 91.162 396 34 1 3943 4337 73794480 73794085 1.840000e-148 536.0
2 TraesCS5D01G123500 chr5D 90.024 411 36 4 3929 4337 553903875 553903468 1.110000e-145 527.0
3 TraesCS5D01G123500 chr5D 96.711 152 5 0 3737 3888 181886413 181886262 2.080000e-63 254.0
4 TraesCS5D01G123500 chr5D 96.711 152 5 0 3891 4042 181886567 181886416 2.080000e-63 254.0
5 TraesCS5D01G123500 chr5D 80.292 274 41 6 3931 4203 114362279 114362540 1.280000e-45 195.0
6 TraesCS5D01G123500 chr5D 77.740 292 53 9 3931 4217 301627276 301626992 7.740000e-38 169.0
7 TraesCS5D01G123500 chr5D 87.302 126 16 0 3582 3707 454312595 454312720 1.300000e-30 145.0
8 TraesCS5D01G123500 chr5D 88.393 112 12 1 3775 3886 553903877 553903767 2.820000e-27 134.0
9 TraesCS5D01G123500 chr5D 89.655 87 9 0 3620 3706 537511319 537511233 1.320000e-20 111.0
10 TraesCS5D01G123500 chr5D 87.640 89 10 1 3618 3705 97272074 97271986 7.960000e-18 102.0
11 TraesCS5D01G123500 chr5D 88.571 70 7 1 3770 3838 488169809 488169878 2.880000e-12 84.2
12 TraesCS5D01G123500 chr5A 93.185 3903 218 18 4 3888 210472670 210476542 0.000000e+00 5690.0
13 TraesCS5D01G123500 chr5A 85.196 1709 210 28 4 1693 349640211 349638527 0.000000e+00 1714.0
14 TraesCS5D01G123500 chr5A 85.821 1072 99 22 827 1897 217403623 217402604 0.000000e+00 1088.0
15 TraesCS5D01G123500 chr5A 91.558 616 35 4 3892 4494 210476380 210476991 0.000000e+00 833.0
16 TraesCS5D01G123500 chr5A 89.916 119 11 1 3589 3707 108623796 108623913 7.790000e-33 152.0
17 TraesCS5D01G123500 chr7B 86.424 1812 226 17 4 1805 24347701 24349502 0.000000e+00 1965.0
18 TraesCS5D01G123500 chr7B 92.719 467 29 3 1431 1896 340677608 340677146 0.000000e+00 669.0
19 TraesCS5D01G123500 chr1D 84.987 1925 249 22 8 1899 154075763 154073846 0.000000e+00 1917.0
20 TraesCS5D01G123500 chr1D 85.311 1559 202 11 2 1534 151374777 151376334 0.000000e+00 1585.0
21 TraesCS5D01G123500 chr1D 84.610 1423 202 12 5 1418 153333479 153332065 0.000000e+00 1399.0
22 TraesCS5D01G123500 chr1D 90.196 408 35 4 3931 4337 70334043 70334446 1.110000e-145 527.0
23 TraesCS5D01G123500 chr1D 79.419 413 82 3 3927 4337 10300387 10299976 5.690000e-74 289.0
24 TraesCS5D01G123500 chr1D 92.308 104 7 1 3778 3881 70334043 70334145 3.630000e-31 147.0
25 TraesCS5D01G123500 chr1D 76.157 281 63 3 4058 4335 223723156 223722877 1.300000e-30 145.0
26 TraesCS5D01G123500 chr1D 86.667 90 11 1 3618 3706 11419430 11419341 1.030000e-16 99.0
27 TraesCS5D01G123500 chr1D 88.710 62 6 1 3931 3992 145931203 145931263 1.740000e-09 75.0
28 TraesCS5D01G123500 chr1D 88.525 61 5 2 3931 3990 267144599 267144540 6.240000e-09 73.1
29 TraesCS5D01G123500 chr5B 85.070 1929 231 34 5 1896 217239238 217237330 0.000000e+00 1914.0
30 TraesCS5D01G123500 chr5B 90.041 482 32 3 3294 3773 152668998 152669465 1.070000e-170 610.0
31 TraesCS5D01G123500 chr5B 91.071 168 15 0 4332 4499 152669511 152669678 1.260000e-55 228.0
32 TraesCS5D01G123500 chr5B 87.500 120 15 0 3589 3708 31114735 31114616 6.070000e-29 139.0
33 TraesCS5D01G123500 chr5B 87.826 115 14 0 3587 3701 434941848 434941734 7.850000e-28 135.0
34 TraesCS5D01G123500 chr5B 87.288 118 15 0 3589 3706 628698492 628698609 7.850000e-28 135.0
35 TraesCS5D01G123500 chr5B 86.441 118 16 0 3589 3706 625118943 625119060 3.650000e-26 130.0
36 TraesCS5D01G123500 chr5B 100.000 37 0 0 3891 3927 152669429 152669465 8.080000e-08 69.4
37 TraesCS5D01G123500 chr7D 85.722 1842 224 23 8 1818 309426590 309424757 0.000000e+00 1908.0
38 TraesCS5D01G123500 chr7D 82.934 1922 268 34 5 1896 207862679 207860788 0.000000e+00 1677.0
39 TraesCS5D01G123500 chr7D 87.621 412 45 3 3927 4337 393036171 393035765 1.460000e-129 473.0
40 TraesCS5D01G123500 chr7D 77.525 396 86 3 3944 4337 40716050 40715656 7.520000e-58 235.0
41 TraesCS5D01G123500 chr7D 90.476 105 9 1 3778 3882 393036167 393036064 2.180000e-28 137.0
42 TraesCS5D01G123500 chr7D 82.353 119 18 3 3586 3703 52243631 52243747 2.860000e-17 100.0
43 TraesCS5D01G123500 chr7D 81.356 118 22 0 3589 3706 280580355 280580238 3.700000e-16 97.1
44 TraesCS5D01G123500 chr4D 86.825 1093 119 9 827 1894 218031204 218032296 0.000000e+00 1197.0
45 TraesCS5D01G123500 chr4D 91.026 78 5 2 3927 4003 272994400 272994324 2.210000e-18 104.0
46 TraesCS5D01G123500 chr1B 82.810 1082 149 25 829 1896 253261490 253262548 0.000000e+00 933.0
47 TraesCS5D01G123500 chr1B 89.189 407 42 2 3932 4337 207376862 207376457 1.440000e-139 507.0
48 TraesCS5D01G123500 chr1B 86.555 119 16 0 3588 3706 50869128 50869010 1.020000e-26 132.0
49 TraesCS5D01G123500 chr3A 84.242 990 121 22 827 1806 330117766 330116802 0.000000e+00 931.0
50 TraesCS5D01G123500 chr3A 91.667 408 32 2 3931 4337 690736981 690737387 8.450000e-157 564.0
51 TraesCS5D01G123500 chr3A 90.991 111 10 0 3778 3888 690736981 690737091 2.800000e-32 150.0
52 TraesCS5D01G123500 chr3A 89.076 119 13 0 3588 3706 272731 272613 1.010000e-31 148.0
53 TraesCS5D01G123500 chr4B 83.131 990 137 17 930 1896 152094938 152093956 0.000000e+00 876.0
54 TraesCS5D01G123500 chr4B 88.675 415 41 5 3928 4337 665325129 665325542 6.720000e-138 501.0
55 TraesCS5D01G123500 chr4B 89.908 109 11 0 3774 3882 665325129 665325237 1.690000e-29 141.0
56 TraesCS5D01G123500 chr3D 84.917 842 113 14 1063 1897 248075503 248076337 0.000000e+00 839.0
57 TraesCS5D01G123500 chr3D 78.293 410 85 4 3931 4337 93488327 93487919 1.240000e-65 261.0
58 TraesCS5D01G123500 chr3D 77.506 409 87 4 3931 4337 582724912 582724507 1.620000e-59 241.0
59 TraesCS5D01G123500 chr3D 77.143 385 81 6 3931 4312 496845640 496845260 2.730000e-52 217.0
60 TraesCS5D01G123500 chr3D 88.288 111 12 1 3777 3886 548509151 548509041 1.020000e-26 132.0
61 TraesCS5D01G123500 chr3D 83.333 120 20 0 3588 3707 168289829 168289710 1.320000e-20 111.0
62 TraesCS5D01G123500 chr3D 89.011 91 9 1 3618 3707 504752722 504752812 1.320000e-20 111.0
63 TraesCS5D01G123500 chr3D 89.024 82 9 0 3626 3707 404320852 404320771 7.960000e-18 102.0
64 TraesCS5D01G123500 chr3D 90.000 50 4 1 3790 3838 615380377 615380328 3.760000e-06 63.9
65 TraesCS5D01G123500 chr7A 90.167 478 35 6 1430 1896 364026820 364026344 2.970000e-171 612.0
66 TraesCS5D01G123500 chr4A 90.663 407 34 3 3932 4337 722781506 722781103 5.120000e-149 538.0
67 TraesCS5D01G123500 chr4A 93.269 104 6 1 3779 3882 722781506 722781404 7.790000e-33 152.0
68 TraesCS5D01G123500 chr2D 90.488 410 36 2 3929 4337 76992938 76993345 5.120000e-149 538.0
69 TraesCS5D01G123500 chr2D 88.924 316 29 5 4023 4337 5949844 5949534 7.060000e-103 385.0
70 TraesCS5D01G123500 chr2D 83.824 408 58 5 3931 4337 147461455 147461855 9.130000e-102 381.0
71 TraesCS5D01G123500 chr2D 89.076 119 13 0 3588 3706 544576132 544576250 1.010000e-31 148.0
72 TraesCS5D01G123500 chr2D 86.667 120 16 0 3587 3706 68862787 68862906 2.820000e-27 134.0
73 TraesCS5D01G123500 chr2D 89.524 105 10 1 3778 3882 76992940 76993043 1.020000e-26 132.0
74 TraesCS5D01G123500 chr2D 83.898 118 19 0 3589 3706 634889172 634889055 3.680000e-21 113.0
75 TraesCS5D01G123500 chr2B 89.487 409 36 3 3930 4337 488046287 488046689 1.120000e-140 510.0
76 TraesCS5D01G123500 chr1A 88.608 395 44 1 3944 4337 130154227 130153833 3.150000e-131 479.0
77 TraesCS5D01G123500 chr1A 90.476 105 9 1 3778 3882 130154238 130154135 2.180000e-28 137.0
78 TraesCS5D01G123500 chr1A 83.158 95 16 0 3778 3872 259075166 259075260 2.230000e-13 87.9
79 TraesCS5D01G123500 chr6D 83.150 273 44 2 3932 4203 436077605 436077876 9.660000e-62 248.0
80 TraesCS5D01G123500 chr6D 75.306 409 83 15 3931 4330 324753426 324753825 3.580000e-41 180.0
81 TraesCS5D01G123500 chr6D 90.476 63 4 2 3931 3992 272799821 272799760 1.040000e-11 82.4
82 TraesCS5D01G123500 chr6D 90.476 63 4 2 3931 3992 272820951 272820890 1.040000e-11 82.4
83 TraesCS5D01G123500 chr6D 90.476 63 5 1 3931 3992 272845562 272845500 1.040000e-11 82.4
84 TraesCS5D01G123500 chr6D 95.652 46 1 1 3944 3988 32240421 32240466 6.240000e-09 73.1
85 TraesCS5D01G123500 chr6D 93.617 47 0 2 3778 3824 450677489 450677532 2.900000e-07 67.6
86 TraesCS5D01G123500 chr2A 89.431 123 12 1 3586 3707 469894926 469895048 2.170000e-33 154.0
87 TraesCS5D01G123500 chr2A 88.235 119 14 0 3588 3706 715299527 715299645 4.690000e-30 143.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G123500 chr5D 181885805 181890303 4498 True 8309.000000 8309 100.0000 1 4499 1 chr5D.!!$R3 4498
1 TraesCS5D01G123500 chr5A 210472670 210476991 4321 False 3261.500000 5690 92.3715 4 4494 2 chr5A.!!$F2 4490
2 TraesCS5D01G123500 chr5A 349638527 349640211 1684 True 1714.000000 1714 85.1960 4 1693 1 chr5A.!!$R2 1689
3 TraesCS5D01G123500 chr5A 217402604 217403623 1019 True 1088.000000 1088 85.8210 827 1897 1 chr5A.!!$R1 1070
4 TraesCS5D01G123500 chr7B 24347701 24349502 1801 False 1965.000000 1965 86.4240 4 1805 1 chr7B.!!$F1 1801
5 TraesCS5D01G123500 chr1D 154073846 154075763 1917 True 1917.000000 1917 84.9870 8 1899 1 chr1D.!!$R4 1891
6 TraesCS5D01G123500 chr1D 151374777 151376334 1557 False 1585.000000 1585 85.3110 2 1534 1 chr1D.!!$F2 1532
7 TraesCS5D01G123500 chr1D 153332065 153333479 1414 True 1399.000000 1399 84.6100 5 1418 1 chr1D.!!$R3 1413
8 TraesCS5D01G123500 chr5B 217237330 217239238 1908 True 1914.000000 1914 85.0700 5 1896 1 chr5B.!!$R2 1891
9 TraesCS5D01G123500 chr5B 152668998 152669678 680 False 302.466667 610 93.7040 3294 4499 3 chr5B.!!$F3 1205
10 TraesCS5D01G123500 chr7D 309424757 309426590 1833 True 1908.000000 1908 85.7220 8 1818 1 chr7D.!!$R4 1810
11 TraesCS5D01G123500 chr7D 207860788 207862679 1891 True 1677.000000 1677 82.9340 5 1896 1 chr7D.!!$R2 1891
12 TraesCS5D01G123500 chr4D 218031204 218032296 1092 False 1197.000000 1197 86.8250 827 1894 1 chr4D.!!$F1 1067
13 TraesCS5D01G123500 chr1B 253261490 253262548 1058 False 933.000000 933 82.8100 829 1896 1 chr1B.!!$F1 1067
14 TraesCS5D01G123500 chr3A 330116802 330117766 964 True 931.000000 931 84.2420 827 1806 1 chr3A.!!$R2 979
15 TraesCS5D01G123500 chr4B 152093956 152094938 982 True 876.000000 876 83.1310 930 1896 1 chr4B.!!$R1 966
16 TraesCS5D01G123500 chr3D 248075503 248076337 834 False 839.000000 839 84.9170 1063 1897 1 chr3D.!!$F1 834

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
911 923 0.461961 AATGACTAGAGCTCGGGCAC 59.538 55.0 18.02 1.98 41.70 5.01 F
2202 2279 0.179020 TGTTGCTGCTAGTGCTTGGT 60.179 50.0 0.00 0.00 40.48 3.67 F
2320 2397 0.111253 AAGGTGGTTGAGGCCTTGAG 59.889 55.0 6.77 0.00 40.71 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2319 2396 0.107831 TAAACGGCCTTCACACTGCT 59.892 50.0 0.0 0.0 0.0 4.24 R
3090 3168 0.322322 ACGGAAGATTAACGGTGCCA 59.678 50.0 0.0 0.0 0.0 4.92 R
3888 3968 0.322456 TTTCACAAGGATCGGCTGGG 60.322 55.0 0.0 0.0 0.0 4.45 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
156 157 3.963647 TCGGACCGCGACGTCAAA 61.964 61.111 17.16 0.00 34.24 2.69
179 180 8.743714 CAAATTCCTAAGCTACTTTTGGAAGAT 58.256 33.333 14.98 7.93 37.83 2.40
564 568 4.466828 CGACCAAGATCAACATCAACAAC 58.533 43.478 0.00 0.00 0.00 3.32
569 573 6.040729 ACCAAGATCAACATCAACAACAATCA 59.959 34.615 0.00 0.00 0.00 2.57
800 804 4.137543 GGTAATGAGGCTTTCAATCCGAT 58.862 43.478 0.00 0.00 39.77 4.18
911 923 0.461961 AATGACTAGAGCTCGGGCAC 59.538 55.000 18.02 1.98 41.70 5.01
1375 1392 1.517832 GACACCGACCCATCTGAGG 59.482 63.158 0.00 0.00 0.00 3.86
1729 1797 2.552315 TCCTTTGTTGTCTTTGGATCGC 59.448 45.455 0.00 0.00 0.00 4.58
1762 1830 4.284829 TGTGTTCATGGATCTAGCACAA 57.715 40.909 0.00 0.00 33.28 3.33
1809 1877 1.772453 TGTTTCCTCTCGTTTCCCCTT 59.228 47.619 0.00 0.00 0.00 3.95
1926 2003 8.574737 CCTTGAAGAAAAAGACTCTCAAATGAT 58.425 33.333 0.00 0.00 0.00 2.45
1973 2050 9.937175 GATGAAGTAATATTTACAGGCTTTGAC 57.063 33.333 0.00 0.00 0.00 3.18
2033 2110 5.161358 TGAACGAACAGTCTGACATGATAC 58.839 41.667 10.88 0.00 0.00 2.24
2064 2141 2.158254 GGTTGGTCTTAGTTTAACGGCG 59.842 50.000 4.80 4.80 0.00 6.46
2079 2156 1.006832 CGGCGGGTCTGTTTATTCTG 58.993 55.000 0.00 0.00 0.00 3.02
2089 2166 4.976116 GTCTGTTTATTCTGTTGGTTGTGC 59.024 41.667 0.00 0.00 0.00 4.57
2156 2233 4.775236 ACCCTAGATTGATTGAGCAGTTC 58.225 43.478 0.00 0.00 0.00 3.01
2180 2257 6.551975 TCCGGACTCTGAATATACAACCAATA 59.448 38.462 0.00 0.00 0.00 1.90
2202 2279 0.179020 TGTTGCTGCTAGTGCTTGGT 60.179 50.000 0.00 0.00 40.48 3.67
2209 2286 1.278985 TGCTAGTGCTTGGTATGCTGT 59.721 47.619 0.00 0.00 40.48 4.40
2214 2291 2.294233 AGTGCTTGGTATGCTGTTGTTG 59.706 45.455 0.00 0.00 0.00 3.33
2229 2306 0.539438 TGTTGTGGGCAAGGATGGAC 60.539 55.000 0.00 0.00 34.94 4.02
2293 2370 6.408092 GGTCATGGTAATGAGGAATGTGAGTA 60.408 42.308 0.00 0.00 43.52 2.59
2310 2387 3.081804 GAGTATGTTCCCAAGGTGGTTG 58.918 50.000 0.00 0.00 35.17 3.77
2311 2388 2.714250 AGTATGTTCCCAAGGTGGTTGA 59.286 45.455 0.00 0.00 38.60 3.18
2312 2389 2.292828 ATGTTCCCAAGGTGGTTGAG 57.707 50.000 0.00 0.00 38.60 3.02
2313 2390 0.184933 TGTTCCCAAGGTGGTTGAGG 59.815 55.000 0.00 0.00 38.60 3.86
2314 2391 1.152830 TTCCCAAGGTGGTTGAGGC 59.847 57.895 0.00 0.00 38.60 4.70
2315 2392 2.283173 CCCAAGGTGGTTGAGGCC 60.283 66.667 0.00 0.00 38.60 5.19
2316 2393 2.845345 CCCAAGGTGGTTGAGGCCT 61.845 63.158 3.86 3.86 38.60 5.19
2317 2394 1.153756 CCAAGGTGGTTGAGGCCTT 59.846 57.895 6.77 0.00 42.77 4.35
2318 2395 4.929807 AAGGTGGTTGAGGCCTTG 57.070 55.556 6.77 0.00 40.71 3.61
2319 2396 2.240510 AAGGTGGTTGAGGCCTTGA 58.759 52.632 6.77 0.00 40.71 3.02
2320 2397 0.111253 AAGGTGGTTGAGGCCTTGAG 59.889 55.000 6.77 0.00 40.71 3.02
2321 2398 1.973812 GGTGGTTGAGGCCTTGAGC 60.974 63.158 6.77 9.25 42.60 4.26
2322 2399 1.228245 GTGGTTGAGGCCTTGAGCA 60.228 57.895 6.77 12.08 46.50 4.26
2332 2409 2.251600 CCTTGAGCAGTGTGAAGGC 58.748 57.895 4.61 0.00 0.00 4.35
2333 2410 1.239968 CCTTGAGCAGTGTGAAGGCC 61.240 60.000 0.00 0.00 0.00 5.19
2334 2411 1.572085 CTTGAGCAGTGTGAAGGCCG 61.572 60.000 0.00 0.00 0.00 6.13
2343 2420 3.370978 CAGTGTGAAGGCCGTTTATGTAG 59.629 47.826 0.00 0.00 0.00 2.74
2349 2426 2.356135 AGGCCGTTTATGTAGCAACTG 58.644 47.619 0.00 0.00 0.00 3.16
2359 2436 8.916654 CGTTTATGTAGCAACTGGAGATTATAG 58.083 37.037 0.00 0.00 0.00 1.31
2364 2441 5.301835 AGCAACTGGAGATTATAGCACAT 57.698 39.130 0.00 0.00 0.00 3.21
2395 2472 3.496884 TCACGCAAAGGTGATGTTTACTC 59.503 43.478 0.00 0.00 41.76 2.59
2500 2577 9.049523 TGCTTAACAAACATGCAATTCAATTTA 57.950 25.926 0.00 0.00 0.00 1.40
2558 2635 0.179129 CAATGCGGGATTCTTGTGGC 60.179 55.000 0.00 0.00 0.00 5.01
2622 2699 8.615878 TGGATTACAAATCCTCAATATTACCG 57.384 34.615 17.27 0.00 38.95 4.02
2694 2771 1.454847 TGGCGGGTGCTTGAGTTTT 60.455 52.632 0.00 0.00 42.25 2.43
2699 2776 1.544759 CGGGTGCTTGAGTTTTAGGGT 60.545 52.381 0.00 0.00 0.00 4.34
2706 2783 6.149633 GTGCTTGAGTTTTAGGGTTTATGTG 58.850 40.000 0.00 0.00 0.00 3.21
2710 2787 6.266168 TGAGTTTTAGGGTTTATGTGCATG 57.734 37.500 0.00 0.00 0.00 4.06
2742 2819 6.879400 AGGGTGTAAGCAAAAACAATTTGTA 58.121 32.000 1.76 0.00 34.77 2.41
2743 2820 7.505258 AGGGTGTAAGCAAAAACAATTTGTAT 58.495 30.769 1.76 0.00 34.77 2.29
2922 3000 6.595682 ACAAGTATAGCTGATATGCCAGTTT 58.404 36.000 0.00 0.00 36.57 2.66
2967 3045 7.549488 AGAGTTATATTCCTTGAAGTTTCCGTG 59.451 37.037 0.00 0.00 0.00 4.94
2980 3058 0.398696 TTCCGTGGAAAGCTAGCCAA 59.601 50.000 12.13 0.00 35.63 4.52
2985 3063 0.605319 TGGAAAGCTAGCCAACACGG 60.605 55.000 12.13 0.00 38.11 4.94
2987 3065 1.303317 AAAGCTAGCCAACACGGGG 60.303 57.895 12.13 0.00 34.06 5.73
3096 3174 3.359695 TGGTTAACCTCTTATGGCACC 57.640 47.619 24.78 0.00 36.82 5.01
3107 3185 4.448210 TCTTATGGCACCGTTAATCTTCC 58.552 43.478 0.00 0.00 0.00 3.46
3113 3191 2.846693 CACCGTTAATCTTCCGTTTGC 58.153 47.619 0.00 0.00 0.00 3.68
3150 3228 5.689819 AGTTTGCGTTGTAAGAATAAGCAG 58.310 37.500 0.00 0.00 34.52 4.24
3159 3237 8.607459 CGTTGTAAGAATAAGCAGAAAGATCAT 58.393 33.333 0.00 0.00 0.00 2.45
3191 3269 7.800300 AATACAAGTCCTTTTAGTCCTCTCT 57.200 36.000 0.00 0.00 0.00 3.10
3237 3315 9.226345 GAATCAATCGTCATTTTCTTTACCATC 57.774 33.333 0.00 0.00 0.00 3.51
3241 3319 9.655769 CAATCGTCATTTTCTTTACCATCTATG 57.344 33.333 0.00 0.00 0.00 2.23
3265 3343 3.320826 GTGCTTTTCCAGGGTAACAACAT 59.679 43.478 0.00 0.00 39.74 2.71
3269 3347 2.198827 TCCAGGGTAACAACATGCAG 57.801 50.000 0.00 0.00 39.74 4.41
3290 3368 0.107654 GCAACGTCCTTAGCCCTGAT 60.108 55.000 0.00 0.00 0.00 2.90
3330 3408 4.780021 AGAGTATGAATGAGAAGGTGGTGT 59.220 41.667 0.00 0.00 0.00 4.16
3343 3421 1.066358 GGTGGTGTAGGTCAGCCTTAC 60.066 57.143 0.00 0.00 44.18 2.34
3607 3687 2.561419 TGTACTCCCTCAGTCCGAAAAG 59.439 50.000 0.00 0.00 36.43 2.27
3609 3689 0.977395 CTCCCTCAGTCCGAAAAGGT 59.023 55.000 0.00 0.00 41.99 3.50
3641 3721 7.201821 CCAAACTTATCCCTCAAATGGATGTAC 60.202 40.741 2.10 0.00 42.57 2.90
3642 3722 6.575244 ACTTATCCCTCAAATGGATGTACA 57.425 37.500 0.00 0.00 42.57 2.90
3648 3728 5.073554 TCCCTCAAATGGATGTACATAGCAT 59.926 40.000 8.71 0.00 0.00 3.79
3674 3754 6.932356 ACTTGGTGCTAGATACATTCATTG 57.068 37.500 0.00 0.00 0.00 2.82
3728 3808 2.558359 CCCTGTTTTGTTGGGTCTCATC 59.442 50.000 0.00 0.00 36.32 2.92
3736 3816 2.300152 TGTTGGGTCTCATCTGTGTCTC 59.700 50.000 0.00 0.00 0.00 3.36
3737 3817 2.300152 GTTGGGTCTCATCTGTGTCTCA 59.700 50.000 0.00 0.00 0.00 3.27
3738 3818 2.174360 TGGGTCTCATCTGTGTCTCAG 58.826 52.381 0.00 0.00 44.85 3.35
3739 3819 1.134848 GGGTCTCATCTGTGTCTCAGC 60.135 57.143 0.00 0.00 43.32 4.26
3740 3820 1.134848 GGTCTCATCTGTGTCTCAGCC 60.135 57.143 0.00 0.00 43.32 4.85
3741 3821 0.813821 TCTCATCTGTGTCTCAGCCG 59.186 55.000 0.00 0.00 43.32 5.52
3742 3822 0.813821 CTCATCTGTGTCTCAGCCGA 59.186 55.000 0.00 0.00 43.32 5.54
3743 3823 1.408340 CTCATCTGTGTCTCAGCCGAT 59.592 52.381 0.00 0.00 43.32 4.18
3744 3824 1.406898 TCATCTGTGTCTCAGCCGATC 59.593 52.381 0.00 0.00 43.32 3.69
3745 3825 0.749649 ATCTGTGTCTCAGCCGATCC 59.250 55.000 0.00 0.00 43.32 3.36
3746 3826 0.323816 TCTGTGTCTCAGCCGATCCT 60.324 55.000 0.00 0.00 43.32 3.24
3747 3827 0.534412 CTGTGTCTCAGCCGATCCTT 59.466 55.000 0.00 0.00 37.36 3.36
3748 3828 0.247460 TGTGTCTCAGCCGATCCTTG 59.753 55.000 0.00 0.00 0.00 3.61
3749 3829 0.247736 GTGTCTCAGCCGATCCTTGT 59.752 55.000 0.00 0.00 0.00 3.16
3750 3830 0.247460 TGTCTCAGCCGATCCTTGTG 59.753 55.000 0.00 0.00 0.00 3.33
3751 3831 0.532573 GTCTCAGCCGATCCTTGTGA 59.467 55.000 0.00 0.00 0.00 3.58
3752 3832 1.066858 GTCTCAGCCGATCCTTGTGAA 60.067 52.381 0.00 0.00 0.00 3.18
3753 3833 1.623311 TCTCAGCCGATCCTTGTGAAA 59.377 47.619 0.00 0.00 0.00 2.69
3754 3834 2.038426 TCTCAGCCGATCCTTGTGAAAA 59.962 45.455 0.00 0.00 0.00 2.29
3755 3835 2.151202 TCAGCCGATCCTTGTGAAAAC 58.849 47.619 0.00 0.00 0.00 2.43
3756 3836 1.879380 CAGCCGATCCTTGTGAAAACA 59.121 47.619 0.00 0.00 0.00 2.83
3757 3837 2.095567 CAGCCGATCCTTGTGAAAACAG 60.096 50.000 0.00 0.00 0.00 3.16
3758 3838 1.880027 GCCGATCCTTGTGAAAACAGT 59.120 47.619 0.00 0.00 0.00 3.55
3759 3839 2.293399 GCCGATCCTTGTGAAAACAGTT 59.707 45.455 0.00 0.00 0.00 3.16
3760 3840 3.500680 GCCGATCCTTGTGAAAACAGTTA 59.499 43.478 0.00 0.00 0.00 2.24
3761 3841 4.612939 GCCGATCCTTGTGAAAACAGTTAC 60.613 45.833 0.00 0.00 0.00 2.50
3762 3842 4.083484 CCGATCCTTGTGAAAACAGTTACC 60.083 45.833 0.00 0.00 0.00 2.85
3763 3843 4.083484 CGATCCTTGTGAAAACAGTTACCC 60.083 45.833 0.00 0.00 0.00 3.69
3764 3844 4.513406 TCCTTGTGAAAACAGTTACCCT 57.487 40.909 0.00 0.00 0.00 4.34
3766 3846 3.243401 CCTTGTGAAAACAGTTACCCTGC 60.243 47.826 0.00 0.00 45.68 4.85
3767 3847 3.006112 TGTGAAAACAGTTACCCTGCA 57.994 42.857 0.00 0.00 45.68 4.41
3768 3848 3.357203 TGTGAAAACAGTTACCCTGCAA 58.643 40.909 0.00 0.00 45.68 4.08
3769 3849 3.380004 TGTGAAAACAGTTACCCTGCAAG 59.620 43.478 0.00 0.00 45.68 4.01
3770 3850 3.630312 GTGAAAACAGTTACCCTGCAAGA 59.370 43.478 0.00 0.00 45.68 3.02
3771 3851 3.630312 TGAAAACAGTTACCCTGCAAGAC 59.370 43.478 0.00 0.00 45.68 3.01
3772 3852 3.290948 AAACAGTTACCCTGCAAGACA 57.709 42.857 0.00 0.00 45.68 3.41
3773 3853 3.508845 AACAGTTACCCTGCAAGACAT 57.491 42.857 0.00 0.00 45.68 3.06
3774 3854 3.508845 ACAGTTACCCTGCAAGACATT 57.491 42.857 0.00 0.00 45.68 2.71
3775 3855 3.149196 ACAGTTACCCTGCAAGACATTG 58.851 45.455 0.00 0.00 45.68 2.82
3776 3856 3.149196 CAGTTACCCTGCAAGACATTGT 58.851 45.455 0.00 0.00 38.76 2.71
3777 3857 3.569701 CAGTTACCCTGCAAGACATTGTT 59.430 43.478 0.00 0.00 38.76 2.83
3778 3858 4.037923 CAGTTACCCTGCAAGACATTGTTT 59.962 41.667 0.00 0.00 38.76 2.83
3779 3859 4.649218 AGTTACCCTGCAAGACATTGTTTT 59.351 37.500 0.00 0.00 38.76 2.43
3780 3860 5.128663 AGTTACCCTGCAAGACATTGTTTTT 59.871 36.000 0.00 0.00 38.76 1.94
3800 3880 4.524316 TTTTTGAGTGAAGGCCATCATG 57.476 40.909 14.79 0.00 0.00 3.07
3801 3881 3.438216 TTTGAGTGAAGGCCATCATGA 57.562 42.857 14.79 0.00 0.00 3.07
3802 3882 2.408271 TGAGTGAAGGCCATCATGAC 57.592 50.000 14.79 9.15 0.00 3.06
3803 3883 1.911357 TGAGTGAAGGCCATCATGACT 59.089 47.619 14.79 6.62 0.00 3.41
3804 3884 3.106827 TGAGTGAAGGCCATCATGACTA 58.893 45.455 14.79 0.00 0.00 2.59
3805 3885 3.133542 TGAGTGAAGGCCATCATGACTAG 59.866 47.826 14.79 0.00 0.00 2.57
3806 3886 2.158842 AGTGAAGGCCATCATGACTAGC 60.159 50.000 14.79 0.63 0.00 3.42
3807 3887 2.121948 TGAAGGCCATCATGACTAGCT 58.878 47.619 6.57 0.00 0.00 3.32
3808 3888 2.507058 TGAAGGCCATCATGACTAGCTT 59.493 45.455 6.57 0.00 0.00 3.74
3809 3889 3.054139 TGAAGGCCATCATGACTAGCTTT 60.054 43.478 6.57 3.93 0.00 3.51
3810 3890 4.164030 TGAAGGCCATCATGACTAGCTTTA 59.836 41.667 6.57 0.00 0.00 1.85
3811 3891 4.989875 AGGCCATCATGACTAGCTTTAT 57.010 40.909 5.01 0.00 0.00 1.40
3812 3892 5.316158 AGGCCATCATGACTAGCTTTATT 57.684 39.130 5.01 0.00 0.00 1.40
3813 3893 6.439636 AGGCCATCATGACTAGCTTTATTA 57.560 37.500 5.01 0.00 0.00 0.98
3814 3894 6.841601 AGGCCATCATGACTAGCTTTATTAA 58.158 36.000 5.01 0.00 0.00 1.40
3815 3895 7.290061 AGGCCATCATGACTAGCTTTATTAAA 58.710 34.615 5.01 0.00 0.00 1.52
3816 3896 7.779798 AGGCCATCATGACTAGCTTTATTAAAA 59.220 33.333 5.01 0.00 0.00 1.52
3817 3897 8.579863 GGCCATCATGACTAGCTTTATTAAAAT 58.420 33.333 0.00 0.00 0.00 1.82
3818 3898 9.971922 GCCATCATGACTAGCTTTATTAAAATT 57.028 29.630 0.00 0.00 0.00 1.82
3838 3918 7.945033 AAATTAAACAATGTTTGCATCGTCT 57.055 28.000 20.40 0.00 33.50 4.18
3839 3919 9.469807 AAAATTAAACAATGTTTGCATCGTCTA 57.530 25.926 20.40 0.00 33.50 2.59
3840 3920 9.638239 AAATTAAACAATGTTTGCATCGTCTAT 57.362 25.926 20.40 0.00 33.50 1.98
3841 3921 8.619146 ATTAAACAATGTTTGCATCGTCTATG 57.381 30.769 20.40 0.00 38.74 2.23
3842 3922 5.878332 AACAATGTTTGCATCGTCTATGA 57.122 34.783 0.00 0.00 37.86 2.15
3843 3923 5.475273 ACAATGTTTGCATCGTCTATGAG 57.525 39.130 0.00 0.00 37.86 2.90
3844 3924 4.201851 ACAATGTTTGCATCGTCTATGAGC 60.202 41.667 0.00 0.00 37.86 4.26
3845 3925 3.251479 TGTTTGCATCGTCTATGAGCT 57.749 42.857 0.00 0.00 37.86 4.09
3846 3926 3.599343 TGTTTGCATCGTCTATGAGCTT 58.401 40.909 0.00 0.00 37.86 3.74
3847 3927 4.754322 TGTTTGCATCGTCTATGAGCTTA 58.246 39.130 0.00 0.00 37.86 3.09
3848 3928 4.566759 TGTTTGCATCGTCTATGAGCTTAC 59.433 41.667 0.00 0.00 37.86 2.34
3849 3929 4.655762 TTGCATCGTCTATGAGCTTACT 57.344 40.909 0.00 0.00 37.86 2.24
3850 3930 5.767816 TTGCATCGTCTATGAGCTTACTA 57.232 39.130 0.00 0.00 37.86 1.82
3851 3931 5.767816 TGCATCGTCTATGAGCTTACTAA 57.232 39.130 0.00 0.00 37.86 2.24
3852 3932 5.520632 TGCATCGTCTATGAGCTTACTAAC 58.479 41.667 0.00 0.00 37.86 2.34
3853 3933 5.067283 TGCATCGTCTATGAGCTTACTAACA 59.933 40.000 0.00 0.00 37.86 2.41
3854 3934 5.977725 GCATCGTCTATGAGCTTACTAACAA 59.022 40.000 0.00 0.00 37.86 2.83
3855 3935 6.074782 GCATCGTCTATGAGCTTACTAACAAC 60.075 42.308 0.00 0.00 37.86 3.32
3856 3936 6.505044 TCGTCTATGAGCTTACTAACAACA 57.495 37.500 0.00 0.00 0.00 3.33
3857 3937 6.320171 TCGTCTATGAGCTTACTAACAACAC 58.680 40.000 0.00 0.00 0.00 3.32
3858 3938 6.072342 TCGTCTATGAGCTTACTAACAACACA 60.072 38.462 0.00 0.00 0.00 3.72
3859 3939 6.251589 CGTCTATGAGCTTACTAACAACACAG 59.748 42.308 0.00 0.00 0.00 3.66
3860 3940 7.091443 GTCTATGAGCTTACTAACAACACAGT 58.909 38.462 0.00 0.00 0.00 3.55
3861 3941 7.273815 GTCTATGAGCTTACTAACAACACAGTC 59.726 40.741 0.00 0.00 0.00 3.51
3862 3942 5.270893 TGAGCTTACTAACAACACAGTCA 57.729 39.130 0.00 0.00 0.00 3.41
3863 3943 5.289595 TGAGCTTACTAACAACACAGTCAG 58.710 41.667 0.00 0.00 0.00 3.51
3864 3944 4.632153 AGCTTACTAACAACACAGTCAGG 58.368 43.478 0.00 0.00 0.00 3.86
3865 3945 4.344102 AGCTTACTAACAACACAGTCAGGA 59.656 41.667 0.00 0.00 0.00 3.86
3866 3946 4.686554 GCTTACTAACAACACAGTCAGGAG 59.313 45.833 0.00 0.00 0.00 3.69
3867 3947 3.753294 ACTAACAACACAGTCAGGAGG 57.247 47.619 0.00 0.00 0.00 4.30
3868 3948 2.224305 ACTAACAACACAGTCAGGAGGC 60.224 50.000 0.00 0.00 0.00 4.70
3869 3949 0.839946 AACAACACAGTCAGGAGGCT 59.160 50.000 0.00 0.00 0.00 4.58
3870 3950 0.394565 ACAACACAGTCAGGAGGCTC 59.605 55.000 5.78 5.78 0.00 4.70
3871 3951 0.668706 CAACACAGTCAGGAGGCTCG 60.669 60.000 8.69 0.00 0.00 5.03
3872 3952 2.125753 CACAGTCAGGAGGCTCGC 60.126 66.667 8.69 1.48 0.00 5.03
3873 3953 3.386237 ACAGTCAGGAGGCTCGCC 61.386 66.667 8.69 0.00 0.00 5.54
3874 3954 4.154347 CAGTCAGGAGGCTCGCCC 62.154 72.222 8.69 0.00 36.58 6.13
3875 3955 4.704103 AGTCAGGAGGCTCGCCCA 62.704 66.667 8.69 0.00 36.58 5.36
3876 3956 3.706373 GTCAGGAGGCTCGCCCAA 61.706 66.667 8.69 0.00 36.58 4.12
3877 3957 3.706373 TCAGGAGGCTCGCCCAAC 61.706 66.667 8.69 0.00 36.58 3.77
3878 3958 4.785453 CAGGAGGCTCGCCCAACC 62.785 72.222 8.69 6.34 36.58 3.77
3880 3960 4.344865 GGAGGCTCGCCCAACCAA 62.345 66.667 8.69 0.00 36.58 3.67
3881 3961 3.056328 GAGGCTCGCCCAACCAAC 61.056 66.667 3.92 0.00 36.58 3.77
3882 3962 4.660938 AGGCTCGCCCAACCAACC 62.661 66.667 3.92 0.00 36.58 3.77
3883 3963 4.966787 GGCTCGCCCAACCAACCA 62.967 66.667 0.00 0.00 0.00 3.67
3884 3964 2.909965 GCTCGCCCAACCAACCAA 60.910 61.111 0.00 0.00 0.00 3.67
3885 3965 2.494530 GCTCGCCCAACCAACCAAA 61.495 57.895 0.00 0.00 0.00 3.28
3886 3966 1.659794 CTCGCCCAACCAACCAAAG 59.340 57.895 0.00 0.00 0.00 2.77
3887 3967 1.805428 CTCGCCCAACCAACCAAAGG 61.805 60.000 0.00 0.00 0.00 3.11
3888 3968 2.425592 GCCCAACCAACCAAAGGC 59.574 61.111 0.00 0.00 0.00 4.35
3889 3969 3.147132 CCCAACCAACCAAAGGCC 58.853 61.111 0.00 0.00 0.00 5.19
4009 4101 4.982999 TCGTCTATGAGCTTACTGACAAC 58.017 43.478 11.40 0.00 0.00 3.32
4016 4108 3.132111 TGAGCTTACTGACAACACAGTCA 59.868 43.478 4.63 0.00 46.36 3.41
4031 4123 2.035442 GTCAGAAGGCTCGCCCAAC 61.035 63.158 3.92 0.00 36.58 3.77
4036 4128 4.660938 AGGCTCGCCCAACCAACC 62.661 66.667 3.92 0.00 36.58 3.77
4112 4204 6.036735 GGTTACAAGAGCGATAACAATGCTTA 59.963 38.462 0.00 0.00 39.49 3.09
4127 4219 4.718940 ATGCTTAAAAATGACCTTCCCG 57.281 40.909 0.00 0.00 0.00 5.14
4167 4259 1.469703 CACATTCTGCGAAGATTGCCA 59.530 47.619 14.05 0.00 0.00 4.92
4171 4263 0.035317 TCTGCGAAGATTGCCACTGT 59.965 50.000 0.00 0.00 0.00 3.55
4182 4274 1.600916 GCCACTGTTGAGTCCCACC 60.601 63.158 0.00 0.00 0.00 4.61
4185 4277 1.611673 CCACTGTTGAGTCCCACCATC 60.612 57.143 0.00 0.00 0.00 3.51
4186 4278 1.349026 CACTGTTGAGTCCCACCATCT 59.651 52.381 0.00 0.00 0.00 2.90
4195 4287 2.572104 AGTCCCACCATCTAGTTTGACC 59.428 50.000 0.00 0.00 0.00 4.02
4254 4347 1.358877 TGCACACGATTGAATCCGAG 58.641 50.000 0.00 0.00 0.00 4.63
4275 4368 6.864165 CCGAGAGAATTAGCAAATACTAGACC 59.136 42.308 0.00 0.00 0.00 3.85
4276 4369 7.426410 CGAGAGAATTAGCAAATACTAGACCA 58.574 38.462 0.00 0.00 0.00 4.02
4313 4406 5.261209 AGCTTCTGTAGTGATGACATCTC 57.739 43.478 16.25 12.58 0.00 2.75
4324 4417 1.266178 TGACATCTCCAGCGAAAGGA 58.734 50.000 0.00 0.00 0.00 3.36
4379 4472 1.641577 GACCATGTCTTGTAGTCCGC 58.358 55.000 0.00 0.00 0.00 5.54
4441 4534 8.604640 TTAACATATTGTGAAACGTACCTTGA 57.395 30.769 0.00 0.00 42.39 3.02
4469 4562 9.887629 TGGTATACTATTTTTATTTCGGTGTGA 57.112 29.630 2.25 0.00 0.00 3.58
4477 4570 0.806868 ATTTCGGTGTGATGCTGCTG 59.193 50.000 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.016444 AGTCCACAACAACAAACACAGAT 58.984 39.130 0.00 0.00 0.00 2.90
156 157 6.319911 GCATCTTCCAAAAGTAGCTTAGGAAT 59.680 38.462 12.76 2.07 37.25 3.01
243 247 0.249573 TCCGGTTCGTGACCTTTGTC 60.250 55.000 0.00 0.00 46.92 3.18
479 483 6.939622 TCTTCATGCACTTTCTTGAGATAGA 58.060 36.000 5.63 0.00 0.00 1.98
564 568 6.385843 TCCGGTGTTTAAAATCATGTGATTG 58.614 36.000 8.86 0.00 43.41 2.67
569 573 5.768164 AGAACTCCGGTGTTTAAAATCATGT 59.232 36.000 21.91 0.00 0.00 3.21
911 923 3.869065 TCACCTTAGTTTCAATAGCCCG 58.131 45.455 0.00 0.00 0.00 6.13
1038 1051 3.861840 CTGTCTTGTCCGTTGGATGTAT 58.138 45.455 0.00 0.00 32.73 2.29
1223 1237 1.613630 AAGCTGGGAGGTGTCGGAT 60.614 57.895 0.00 0.00 0.00 4.18
1463 1508 3.480133 GGTACATGGGCCTCGGCT 61.480 66.667 4.53 0.00 41.60 5.52
1729 1797 3.251729 CCATGAACACAAAGAGGTCACAG 59.748 47.826 0.00 0.00 0.00 3.66
1809 1877 2.011222 GAACACACGAGGGAAAACACA 58.989 47.619 0.00 0.00 0.00 3.72
2024 2101 9.209175 GACCAACCATTAGAATAGTATCATGTC 57.791 37.037 0.00 0.00 0.00 3.06
2060 2137 1.006832 CAGAATAAACAGACCCGCCG 58.993 55.000 0.00 0.00 0.00 6.46
2064 2141 4.583073 ACAACCAACAGAATAAACAGACCC 59.417 41.667 0.00 0.00 0.00 4.46
2079 2156 2.858745 TCCTCCTAAAGCACAACCAAC 58.141 47.619 0.00 0.00 0.00 3.77
2089 2166 2.095461 GGCCAAGCTTTCCTCCTAAAG 58.905 52.381 0.00 0.00 39.10 1.85
2156 2233 4.665833 TGGTTGTATATTCAGAGTCCGG 57.334 45.455 0.00 0.00 0.00 5.14
2180 2257 1.605710 CAAGCACTAGCAGCAACAACT 59.394 47.619 10.05 0.00 45.49 3.16
2193 2270 2.276732 ACAACAGCATACCAAGCACT 57.723 45.000 0.00 0.00 0.00 4.40
2202 2279 1.612950 CTTGCCCACAACAACAGCATA 59.387 47.619 0.00 0.00 32.67 3.14
2209 2286 0.187117 TCCATCCTTGCCCACAACAA 59.813 50.000 0.00 0.00 0.00 2.83
2214 2291 1.450312 CTCGTCCATCCTTGCCCAC 60.450 63.158 0.00 0.00 0.00 4.61
2229 2306 0.523072 CATCCCCAAGTGCAAACTCG 59.477 55.000 0.00 0.00 0.00 4.18
2293 2370 1.203050 CCTCAACCACCTTGGGAACAT 60.203 52.381 0.00 0.00 43.37 2.71
2310 2387 0.250467 TTCACACTGCTCAAGGCCTC 60.250 55.000 5.23 0.00 40.92 4.70
2311 2388 0.250640 CTTCACACTGCTCAAGGCCT 60.251 55.000 0.00 0.00 40.92 5.19
2312 2389 1.239968 CCTTCACACTGCTCAAGGCC 61.240 60.000 0.00 0.00 40.92 5.19
2313 2390 2.251600 CCTTCACACTGCTCAAGGC 58.748 57.895 0.00 0.00 42.22 4.35
2314 2391 1.239968 GGCCTTCACACTGCTCAAGG 61.240 60.000 0.00 0.00 38.82 3.61
2315 2392 1.572085 CGGCCTTCACACTGCTCAAG 61.572 60.000 0.00 0.00 0.00 3.02
2316 2393 1.597854 CGGCCTTCACACTGCTCAA 60.598 57.895 0.00 0.00 0.00 3.02
2317 2394 2.031012 CGGCCTTCACACTGCTCA 59.969 61.111 0.00 0.00 0.00 4.26
2318 2395 1.166531 AAACGGCCTTCACACTGCTC 61.167 55.000 0.00 0.00 0.00 4.26
2319 2396 0.107831 TAAACGGCCTTCACACTGCT 59.892 50.000 0.00 0.00 0.00 4.24
2320 2397 1.135689 CATAAACGGCCTTCACACTGC 60.136 52.381 0.00 0.00 0.00 4.40
2321 2398 2.151202 ACATAAACGGCCTTCACACTG 58.849 47.619 0.00 0.00 0.00 3.66
2322 2399 2.561478 ACATAAACGGCCTTCACACT 57.439 45.000 0.00 0.00 0.00 3.55
2332 2409 3.857052 TCTCCAGTTGCTACATAAACGG 58.143 45.455 0.13 0.00 0.00 4.44
2333 2410 7.715265 ATAATCTCCAGTTGCTACATAAACG 57.285 36.000 0.13 0.00 0.00 3.60
2334 2411 8.713271 GCTATAATCTCCAGTTGCTACATAAAC 58.287 37.037 0.13 0.00 0.00 2.01
2343 2420 6.382869 AAATGTGCTATAATCTCCAGTTGC 57.617 37.500 0.00 0.00 0.00 4.17
2364 2441 3.628032 TCACCTTTGCGTGACACAATAAA 59.372 39.130 6.37 3.02 37.85 1.40
2376 2453 2.478894 ACGAGTAAACATCACCTTTGCG 59.521 45.455 0.00 0.00 0.00 4.85
2395 2472 1.877637 TGACTCACCACATCCAAACG 58.122 50.000 0.00 0.00 0.00 3.60
2504 2581 9.603921 GTAGGCCAACTAAACTAATACATACAA 57.396 33.333 5.01 0.00 32.37 2.41
2520 2597 4.574674 TTGATGATCAAGTAGGCCAACT 57.425 40.909 5.01 0.00 31.83 3.16
2597 2674 8.433599 TCGGTAATATTGAGGATTTGTAATCCA 58.566 33.333 18.02 1.31 40.61 3.41
2635 2712 7.443575 GCTCTTCCTTGTATGATCATAATGTGT 59.556 37.037 16.97 0.00 0.00 3.72
2675 2752 1.734388 AAAACTCAAGCACCCGCCAC 61.734 55.000 0.00 0.00 39.83 5.01
2682 2759 6.149633 CACATAAACCCTAAAACTCAAGCAC 58.850 40.000 0.00 0.00 0.00 4.40
2694 2771 4.518278 ATGGACATGCACATAAACCCTA 57.482 40.909 0.00 0.00 0.00 3.53
2699 2776 6.003326 CACCCTATATGGACATGCACATAAA 58.997 40.000 12.30 0.00 38.35 1.40
2706 2783 4.003648 GCTTACACCCTATATGGACATGC 58.996 47.826 0.45 0.00 38.35 4.06
2710 2787 6.376018 TGTTTTTGCTTACACCCTATATGGAC 59.624 38.462 0.45 0.00 38.35 4.02
2742 2819 7.976734 CCAAATCTCTCTCGTAAGTTTAGTCAT 59.023 37.037 0.00 0.00 39.48 3.06
2743 2820 7.039923 ACCAAATCTCTCTCGTAAGTTTAGTCA 60.040 37.037 0.00 0.00 39.48 3.41
2751 2828 6.647067 ACTCAAAACCAAATCTCTCTCGTAAG 59.353 38.462 0.00 0.00 0.00 2.34
2791 2868 8.692710 ACTATCATAGGAGTTACAATCGAACAA 58.307 33.333 0.00 0.00 0.00 2.83
2947 3025 5.174037 TCCACGGAAACTTCAAGGAATAT 57.826 39.130 0.00 0.00 0.00 1.28
2967 3045 1.305930 CCCGTGTTGGCTAGCTTTCC 61.306 60.000 15.72 0.00 35.87 3.13
2980 3058 0.107214 CACATCCAATAGCCCCGTGT 60.107 55.000 0.00 0.00 0.00 4.49
2985 3063 2.638480 TAGTGCACATCCAATAGCCC 57.362 50.000 21.04 0.00 0.00 5.19
2987 3065 6.652481 AGATACAATAGTGCACATCCAATAGC 59.348 38.462 21.04 6.88 0.00 2.97
3054 3132 8.527567 ACCAACCGAACAAAAACATAATATTG 57.472 30.769 0.00 0.00 0.00 1.90
3090 3168 0.322322 ACGGAAGATTAACGGTGCCA 59.678 50.000 0.00 0.00 0.00 4.92
3096 3174 4.600012 ATCTGCAAACGGAAGATTAACG 57.400 40.909 0.00 0.00 38.94 3.18
3107 3185 7.439490 CAAACTAAAGCAATTATCTGCAAACG 58.561 34.615 0.00 0.00 45.18 3.60
3113 3191 6.582295 ACAACGCAAACTAAAGCAATTATCTG 59.418 34.615 0.00 0.00 0.00 2.90
3167 3245 7.800300 AGAGAGGACTAAAAGGACTTGTATT 57.200 36.000 0.00 0.00 0.00 1.89
3191 3269 9.448438 TTGATTCAGAAGTAGCAAGCTAAATTA 57.552 29.630 2.92 0.00 0.00 1.40
3237 3315 2.795329 ACCCTGGAAAAGCACACATAG 58.205 47.619 0.00 0.00 0.00 2.23
3241 3319 2.303175 TGTTACCCTGGAAAAGCACAC 58.697 47.619 0.00 0.00 0.00 3.82
3265 3343 0.670546 GCTAAGGACGTTGCTCTGCA 60.671 55.000 0.00 0.00 36.47 4.41
3269 3347 0.741221 CAGGGCTAAGGACGTTGCTC 60.741 60.000 0.00 0.00 0.00 4.26
3290 3368 0.750249 TCTGCAACGAAGTCACCTGA 59.250 50.000 0.00 0.00 45.00 3.86
3648 3728 8.892723 CAATGAATGTATCTAGCACCAAGTTAA 58.107 33.333 0.00 0.00 0.00 2.01
3674 3754 1.892209 TCGAAAAAGCTTGTCCCTCC 58.108 50.000 0.00 0.00 0.00 4.30
3714 3794 2.705658 AGACACAGATGAGACCCAACAA 59.294 45.455 0.00 0.00 0.00 2.83
3736 3816 1.879380 TGTTTTCACAAGGATCGGCTG 59.121 47.619 0.00 0.00 0.00 4.85
3737 3817 2.154462 CTGTTTTCACAAGGATCGGCT 58.846 47.619 0.00 0.00 30.36 5.52
3738 3818 1.880027 ACTGTTTTCACAAGGATCGGC 59.120 47.619 0.00 0.00 30.36 5.54
3739 3819 4.083484 GGTAACTGTTTTCACAAGGATCGG 60.083 45.833 0.00 0.00 30.36 4.18
3740 3820 4.083484 GGGTAACTGTTTTCACAAGGATCG 60.083 45.833 0.00 0.00 30.36 3.69
3741 3821 5.048713 CAGGGTAACTGTTTTCACAAGGATC 60.049 44.000 0.00 0.00 42.42 3.36
3742 3822 4.827284 CAGGGTAACTGTTTTCACAAGGAT 59.173 41.667 0.00 0.00 42.42 3.24
3743 3823 4.204012 CAGGGTAACTGTTTTCACAAGGA 58.796 43.478 0.00 0.00 42.42 3.36
3744 3824 4.568152 CAGGGTAACTGTTTTCACAAGG 57.432 45.455 0.00 0.00 42.42 3.61
3756 3836 3.508845 ACAATGTCTTGCAGGGTAACT 57.491 42.857 0.00 0.00 35.69 2.24
3757 3837 4.584327 AAACAATGTCTTGCAGGGTAAC 57.416 40.909 0.00 0.00 35.69 2.50
3758 3838 5.606348 AAAAACAATGTCTTGCAGGGTAA 57.394 34.783 0.00 0.00 35.69 2.85
3779 3859 4.022068 GTCATGATGGCCTTCACTCAAAAA 60.022 41.667 22.61 0.00 0.00 1.94
3780 3860 3.507233 GTCATGATGGCCTTCACTCAAAA 59.493 43.478 22.61 0.00 0.00 2.44
3781 3861 3.084039 GTCATGATGGCCTTCACTCAAA 58.916 45.455 22.61 5.06 0.00 2.69
3782 3862 2.306805 AGTCATGATGGCCTTCACTCAA 59.693 45.455 22.61 6.71 0.00 3.02
3783 3863 1.911357 AGTCATGATGGCCTTCACTCA 59.089 47.619 22.61 8.93 0.00 3.41
3784 3864 2.706339 AGTCATGATGGCCTTCACTC 57.294 50.000 22.61 15.10 0.00 3.51
3785 3865 2.158842 GCTAGTCATGATGGCCTTCACT 60.159 50.000 22.61 17.06 0.00 3.41
3786 3866 2.158842 AGCTAGTCATGATGGCCTTCAC 60.159 50.000 22.61 11.00 0.00 3.18
3787 3867 2.121948 AGCTAGTCATGATGGCCTTCA 58.878 47.619 22.42 22.42 0.00 3.02
3788 3868 2.926778 AGCTAGTCATGATGGCCTTC 57.073 50.000 11.69 11.69 0.00 3.46
3789 3869 3.659183 AAAGCTAGTCATGATGGCCTT 57.341 42.857 3.32 0.00 0.00 4.35
3790 3870 4.989875 ATAAAGCTAGTCATGATGGCCT 57.010 40.909 3.32 0.00 0.00 5.19
3791 3871 7.510549 TTTAATAAAGCTAGTCATGATGGCC 57.489 36.000 0.00 0.00 0.00 5.36
3792 3872 9.971922 AATTTTAATAAAGCTAGTCATGATGGC 57.028 29.630 0.00 4.04 0.00 4.40
3822 3902 4.034858 AGCTCATAGACGATGCAAACATTG 59.965 41.667 0.00 0.00 42.60 2.82
3823 3903 4.194640 AGCTCATAGACGATGCAAACATT 58.805 39.130 0.00 0.00 36.35 2.71
3824 3904 3.801698 AGCTCATAGACGATGCAAACAT 58.198 40.909 0.00 0.00 39.98 2.71
3825 3905 3.251479 AGCTCATAGACGATGCAAACA 57.749 42.857 0.00 0.00 35.29 2.83
3826 3906 4.806247 AGTAAGCTCATAGACGATGCAAAC 59.194 41.667 0.00 0.00 35.29 2.93
3827 3907 5.011090 AGTAAGCTCATAGACGATGCAAA 57.989 39.130 0.00 0.00 35.29 3.68
3828 3908 4.655762 AGTAAGCTCATAGACGATGCAA 57.344 40.909 0.00 0.00 35.29 4.08
3829 3909 5.067283 TGTTAGTAAGCTCATAGACGATGCA 59.933 40.000 0.00 0.00 35.29 3.96
3830 3910 5.520632 TGTTAGTAAGCTCATAGACGATGC 58.479 41.667 0.00 0.00 35.29 3.91
3831 3911 6.972901 TGTTGTTAGTAAGCTCATAGACGATG 59.027 38.462 0.00 0.00 36.82 3.84
3832 3912 6.973474 GTGTTGTTAGTAAGCTCATAGACGAT 59.027 38.462 0.00 0.00 0.00 3.73
3833 3913 6.072342 TGTGTTGTTAGTAAGCTCATAGACGA 60.072 38.462 0.00 0.00 0.00 4.20
3834 3914 6.090783 TGTGTTGTTAGTAAGCTCATAGACG 58.909 40.000 0.00 0.00 0.00 4.18
3835 3915 7.091443 ACTGTGTTGTTAGTAAGCTCATAGAC 58.909 38.462 0.00 0.00 0.00 2.59
3836 3916 7.039993 TGACTGTGTTGTTAGTAAGCTCATAGA 60.040 37.037 0.00 0.00 0.00 1.98
3837 3917 7.090808 TGACTGTGTTGTTAGTAAGCTCATAG 58.909 38.462 0.00 0.00 0.00 2.23
3838 3918 6.988522 TGACTGTGTTGTTAGTAAGCTCATA 58.011 36.000 0.00 0.00 0.00 2.15
3839 3919 5.853936 TGACTGTGTTGTTAGTAAGCTCAT 58.146 37.500 0.00 0.00 0.00 2.90
3840 3920 5.270893 TGACTGTGTTGTTAGTAAGCTCA 57.729 39.130 0.00 0.00 0.00 4.26
3841 3921 4.686554 CCTGACTGTGTTGTTAGTAAGCTC 59.313 45.833 0.00 0.00 0.00 4.09
3842 3922 4.344102 TCCTGACTGTGTTGTTAGTAAGCT 59.656 41.667 0.00 0.00 0.00 3.74
3843 3923 4.628074 TCCTGACTGTGTTGTTAGTAAGC 58.372 43.478 0.00 0.00 0.00 3.09
3844 3924 5.230942 CCTCCTGACTGTGTTGTTAGTAAG 58.769 45.833 0.00 0.00 0.00 2.34
3845 3925 4.502604 GCCTCCTGACTGTGTTGTTAGTAA 60.503 45.833 0.00 0.00 0.00 2.24
3846 3926 3.006537 GCCTCCTGACTGTGTTGTTAGTA 59.993 47.826 0.00 0.00 0.00 1.82
3847 3927 2.224305 GCCTCCTGACTGTGTTGTTAGT 60.224 50.000 0.00 0.00 0.00 2.24
3848 3928 2.037772 AGCCTCCTGACTGTGTTGTTAG 59.962 50.000 0.00 0.00 0.00 2.34
3849 3929 2.037251 GAGCCTCCTGACTGTGTTGTTA 59.963 50.000 0.00 0.00 0.00 2.41
3850 3930 0.839946 AGCCTCCTGACTGTGTTGTT 59.160 50.000 0.00 0.00 0.00 2.83
3851 3931 0.394565 GAGCCTCCTGACTGTGTTGT 59.605 55.000 0.00 0.00 0.00 3.32
3852 3932 0.668706 CGAGCCTCCTGACTGTGTTG 60.669 60.000 0.00 0.00 0.00 3.33
3853 3933 1.668294 CGAGCCTCCTGACTGTGTT 59.332 57.895 0.00 0.00 0.00 3.32
3854 3934 2.936912 GCGAGCCTCCTGACTGTGT 61.937 63.158 0.00 0.00 0.00 3.72
3855 3935 2.125753 GCGAGCCTCCTGACTGTG 60.126 66.667 0.00 0.00 0.00 3.66
3856 3936 3.386237 GGCGAGCCTCCTGACTGT 61.386 66.667 6.90 0.00 0.00 3.55
3857 3937 4.154347 GGGCGAGCCTCCTGACTG 62.154 72.222 14.33 0.00 36.10 3.51
3858 3938 4.704103 TGGGCGAGCCTCCTGACT 62.704 66.667 14.33 0.00 36.10 3.41
3859 3939 3.706373 TTGGGCGAGCCTCCTGAC 61.706 66.667 14.33 0.00 36.10 3.51
3860 3940 3.706373 GTTGGGCGAGCCTCCTGA 61.706 66.667 14.33 0.00 36.10 3.86
3861 3941 4.785453 GGTTGGGCGAGCCTCCTG 62.785 72.222 14.33 0.00 36.10 3.86
3863 3943 4.344865 TTGGTTGGGCGAGCCTCC 62.345 66.667 14.33 13.69 36.10 4.30
3864 3944 3.056328 GTTGGTTGGGCGAGCCTC 61.056 66.667 14.33 4.95 36.10 4.70
3865 3945 4.660938 GGTTGGTTGGGCGAGCCT 62.661 66.667 14.33 0.00 36.10 4.58
3866 3946 4.966787 TGGTTGGTTGGGCGAGCC 62.967 66.667 5.37 5.37 0.00 4.70
3867 3947 2.420466 CTTTGGTTGGTTGGGCGAGC 62.420 60.000 0.00 0.00 0.00 5.03
3868 3948 1.659794 CTTTGGTTGGTTGGGCGAG 59.340 57.895 0.00 0.00 0.00 5.03
3869 3949 1.830408 CCTTTGGTTGGTTGGGCGA 60.830 57.895 0.00 0.00 0.00 5.54
3870 3950 2.733945 CCTTTGGTTGGTTGGGCG 59.266 61.111 0.00 0.00 0.00 6.13
3871 3951 2.425592 GCCTTTGGTTGGTTGGGC 59.574 61.111 0.00 0.00 0.00 5.36
3872 3952 2.515979 GGGCCTTTGGTTGGTTGGG 61.516 63.158 0.84 0.00 0.00 4.12
3873 3953 1.757423 CTGGGCCTTTGGTTGGTTGG 61.757 60.000 4.53 0.00 0.00 3.77
3874 3954 1.747774 CTGGGCCTTTGGTTGGTTG 59.252 57.895 4.53 0.00 0.00 3.77
3875 3955 2.140138 GCTGGGCCTTTGGTTGGTT 61.140 57.895 4.53 0.00 0.00 3.67
3876 3956 2.524148 GCTGGGCCTTTGGTTGGT 60.524 61.111 4.53 0.00 0.00 3.67
3877 3957 3.313524 GGCTGGGCCTTTGGTTGG 61.314 66.667 4.53 0.00 46.69 3.77
3886 3966 4.115199 ACAAGGATCGGCTGGGCC 62.115 66.667 0.00 0.00 46.75 5.80
3887 3967 2.819984 TTCACAAGGATCGGCTGGGC 62.820 60.000 0.00 0.00 0.00 5.36
3888 3968 0.322456 TTTCACAAGGATCGGCTGGG 60.322 55.000 0.00 0.00 0.00 4.45
3889 3969 1.533625 TTTTCACAAGGATCGGCTGG 58.466 50.000 0.00 0.00 0.00 4.85
4009 4101 1.739562 GGCGAGCCTTCTGACTGTG 60.740 63.158 6.90 0.00 0.00 3.66
4016 4108 2.829384 TTGGTTGGGCGAGCCTTCT 61.829 57.895 14.33 0.00 36.10 2.85
4018 4110 2.597510 GTTGGTTGGGCGAGCCTT 60.598 61.111 14.33 0.00 36.10 4.35
4031 4123 6.889722 TCTGTAATAAATCCTCCTTTGGTTGG 59.110 38.462 0.00 0.00 0.00 3.77
4064 4156 1.676746 CAGCTCATGTGCTAGCCAAT 58.323 50.000 21.05 2.54 41.98 3.16
4067 4159 3.418714 GCAGCTCATGTGCTAGCC 58.581 61.111 21.05 9.63 41.98 3.93
4112 4204 3.763897 CCTTGATCGGGAAGGTCATTTTT 59.236 43.478 2.75 0.00 40.16 1.94
4127 4219 6.222038 TGTGTGGATACTAGTTCCTTGATC 57.778 41.667 18.78 8.47 34.17 2.92
4171 4263 3.907474 TCAAACTAGATGGTGGGACTCAA 59.093 43.478 0.00 0.00 0.00 3.02
4220 4312 2.421424 GTGTGCATTGGAATCAGACTCC 59.579 50.000 0.00 0.00 0.00 3.85
4233 4325 2.352651 CTCGGATTCAATCGTGTGCATT 59.647 45.455 0.00 0.00 0.00 3.56
4234 4326 1.935873 CTCGGATTCAATCGTGTGCAT 59.064 47.619 0.00 0.00 0.00 3.96
4236 4328 1.590238 CTCTCGGATTCAATCGTGTGC 59.410 52.381 0.00 0.00 0.00 4.57
4254 4347 9.418045 GAGATGGTCTAGTATTTGCTAATTCTC 57.582 37.037 3.50 1.60 0.00 2.87
4275 4368 3.695060 AGAAGCTTTGGCAATGAGAGATG 59.305 43.478 16.43 0.00 41.70 2.90
4276 4369 3.695060 CAGAAGCTTTGGCAATGAGAGAT 59.305 43.478 16.43 0.00 41.70 2.75
4313 4406 4.493547 TGCAAATTTATTCCTTTCGCTGG 58.506 39.130 0.00 0.00 0.00 4.85
4379 4472 5.443185 TCAACTGCTCATTTTTCAAGGAG 57.557 39.130 0.00 0.00 42.66 3.69
4464 4557 0.664761 ACAACACAGCAGCATCACAC 59.335 50.000 0.00 0.00 0.00 3.82


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

AutoCloner maintained by Alex Coulton.