Multiple sequence alignment - TraesCS2D01G127800

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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 TraesCS2D01G127800 chr2D 100.000 4602 0 0 1 4602 74282936 74278335 0.000000e+00 8499.0
1 TraesCS2D01G127800 chr2D 97.895 95 2 0 4449 4543 74278581 74278487 1.020000e-36 165.0
2 TraesCS2D01G127800 chr2D 81.935 155 14 7 4455 4597 197687624 197687472 8.090000e-23 119.0
3 TraesCS2D01G127800 chr2D 97.872 47 1 0 2101 2147 26618724 26618770 1.060000e-11 82.4
4 TraesCS2D01G127800 chr2D 92.453 53 4 0 2102 2154 619480838 619480786 4.940000e-10 76.8
5 TraesCS2D01G127800 chr2A 96.304 1894 60 5 2 1892 73558012 73556126 0.000000e+00 3101.0
6 TraesCS2D01G127800 chr2A 93.757 897 24 3 2034 2916 73556113 73555235 0.000000e+00 1317.0
7 TraesCS2D01G127800 chr2A 92.522 682 38 7 3078 3746 73555071 73554390 0.000000e+00 965.0
8 TraesCS2D01G127800 chr2A 79.971 679 89 29 2686 3355 383426662 383426022 1.510000e-124 457.0
9 TraesCS2D01G127800 chr2A 90.283 247 21 3 1859 2103 310535638 310535883 2.070000e-83 320.0
10 TraesCS2D01G127800 chr2A 87.671 73 5 1 2075 2147 73556128 73556196 1.060000e-11 82.4
11 TraesCS2D01G127800 chr2B 96.667 1620 29 11 2238 3843 113327083 113325475 0.000000e+00 2669.0
12 TraesCS2D01G127800 chr2B 96.239 904 24 8 944 1841 113327976 113327077 0.000000e+00 1472.0
13 TraesCS2D01G127800 chr2B 94.690 565 23 3 4045 4602 113324109 113323545 0.000000e+00 870.0
14 TraesCS2D01G127800 chr2B 91.632 239 9 2 3823 4050 113324403 113324165 2.070000e-83 320.0
15 TraesCS2D01G127800 chr2B 94.737 95 5 0 4449 4543 113323791 113323697 1.030000e-31 148.0
16 TraesCS2D01G127800 chr2B 79.464 224 30 8 684 901 728957962 728957749 1.330000e-30 145.0
17 TraesCS2D01G127800 chr3B 91.705 1314 70 12 2450 3746 114144818 114143527 0.000000e+00 1786.0
18 TraesCS2D01G127800 chr3B 91.741 896 51 13 942 1822 114145954 114145067 0.000000e+00 1223.0
19 TraesCS2D01G127800 chr3B 90.262 267 24 1 4184 4450 293788858 293788594 9.480000e-92 348.0
20 TraesCS2D01G127800 chr3B 88.764 267 28 1 4184 4450 293955464 293955200 4.440000e-85 326.0
21 TraesCS2D01G127800 chr3B 89.919 248 24 1 1858 2105 815642068 815642314 7.430000e-83 318.0
22 TraesCS2D01G127800 chr3B 95.798 119 5 0 3748 3866 114142505 114142387 4.700000e-45 193.0
23 TraesCS2D01G127800 chr3B 89.655 116 10 2 2157 2270 114145057 114144942 3.710000e-31 147.0
24 TraesCS2D01G127800 chr3B 85.393 89 12 1 371 459 114146282 114146195 1.760000e-14 91.6
25 TraesCS2D01G127800 chr3B 84.722 72 9 2 2102 2172 483399659 483399729 2.300000e-08 71.3
26 TraesCS2D01G127800 chr3D 88.612 1326 84 23 2446 3746 67711664 67712947 0.000000e+00 1550.0
27 TraesCS2D01G127800 chr3D 90.677 901 55 16 942 1822 67710406 67711297 0.000000e+00 1171.0
28 TraesCS2D01G127800 chr3D 86.544 327 20 8 3748 4050 67713972 67714298 5.700000e-89 339.0
29 TraesCS2D01G127800 chr3D 89.256 242 22 4 4184 4425 48824565 48824802 2.690000e-77 300.0
30 TraesCS2D01G127800 chr3D 92.593 54 4 0 2102 2155 424659626 424659573 1.370000e-10 78.7
31 TraesCS2D01G127800 chr3D 92.308 52 4 0 2105 2156 565995260 565995311 1.780000e-09 75.0
32 TraesCS2D01G127800 chr3A 88.124 1322 92 21 2450 3746 79401536 79402817 0.000000e+00 1511.0
33 TraesCS2D01G127800 chr3A 93.555 481 26 5 942 1418 79400439 79400918 0.000000e+00 712.0
34 TraesCS2D01G127800 chr3A 88.220 382 30 5 1443 1822 79400901 79401269 4.230000e-120 442.0
35 TraesCS2D01G127800 chr3A 77.706 462 65 19 2816 3271 585936700 585936271 9.890000e-62 248.0
36 TraesCS2D01G127800 chr3A 90.972 144 10 2 3748 3891 79403852 79403992 1.690000e-44 191.0
37 TraesCS2D01G127800 chr3A 93.103 87 6 0 3959 4045 79404468 79404554 1.340000e-25 128.0
38 TraesCS2D01G127800 chr6B 79.250 800 129 26 2560 3352 116891589 116892358 1.470000e-144 523.0
39 TraesCS2D01G127800 chr6B 83.855 415 58 8 2560 2972 28008629 28009036 2.010000e-103 387.0
40 TraesCS2D01G127800 chr6B 88.679 53 6 0 683 735 580243366 580243314 1.070000e-06 65.8
41 TraesCS2D01G127800 chr5B 91.498 247 20 1 1858 2103 115053978 115054224 5.700000e-89 339.0
42 TraesCS2D01G127800 chr5B 98.077 52 0 1 1812 1862 55371928 55371877 6.340000e-14 89.8
43 TraesCS2D01G127800 chr5B 94.340 53 3 0 2102 2154 269975194 269975246 1.060000e-11 82.4
44 TraesCS2D01G127800 chr1D 90.551 254 23 1 1853 2105 4974454 4974707 7.380000e-88 335.0
45 TraesCS2D01G127800 chr1D 90.323 248 22 2 1858 2103 29961487 29961240 1.600000e-84 324.0
46 TraesCS2D01G127800 chr1D 89.243 251 21 4 4180 4429 312670162 312670407 4.470000e-80 309.0
47 TraesCS2D01G127800 chr1D 81.410 156 15 7 4454 4597 15530034 15529881 1.050000e-21 115.0
48 TraesCS2D01G127800 chr1D 80.000 155 17 7 4455 4597 125266446 125266294 8.150000e-18 102.0
49 TraesCS2D01G127800 chr1D 79.870 154 17 7 4456 4597 15524878 15524727 2.930000e-17 100.0
50 TraesCS2D01G127800 chr1D 94.000 50 3 0 2102 2151 111540705 111540754 4.940000e-10 76.8
51 TraesCS2D01G127800 chr1D 95.652 46 2 0 2102 2147 211494708 211494753 1.780000e-09 75.0
52 TraesCS2D01G127800 chr1D 95.652 46 2 0 2102 2147 346659756 346659711 1.780000e-09 75.0
53 TraesCS2D01G127800 chr1D 90.741 54 5 0 2102 2155 251301848 251301795 6.390000e-09 73.1
54 TraesCS2D01G127800 chr6D 91.093 247 20 2 1859 2103 363386185 363386431 2.650000e-87 333.0
55 TraesCS2D01G127800 chr6D 86.940 268 29 4 4184 4450 380427526 380427264 3.480000e-76 296.0
56 TraesCS2D01G127800 chr6D 83.660 153 21 1 4449 4597 380427358 380427206 1.730000e-29 141.0
57 TraesCS2D01G127800 chr6D 82.692 156 13 7 4454 4597 364244786 364244633 4.830000e-25 126.0
58 TraesCS2D01G127800 chr6D 98.077 52 1 0 2391 2442 43988042 43988093 1.760000e-14 91.6
59 TraesCS2D01G127800 chr6D 97.778 45 1 0 2103 2147 103006170 103006126 1.370000e-10 78.7
60 TraesCS2D01G127800 chr6D 97.674 43 1 0 2104 2146 462439541 462439499 1.780000e-09 75.0
61 TraesCS2D01G127800 chr6D 91.837 49 4 0 2108 2156 81224559 81224607 8.260000e-08 69.4
62 TraesCS2D01G127800 chr6D 93.478 46 3 0 2102 2147 431050480 431050525 8.260000e-08 69.4
63 TraesCS2D01G127800 chr6D 87.719 57 6 1 2108 2163 7865955 7865899 1.070000e-06 65.8
64 TraesCS2D01G127800 chr6A 89.139 267 24 3 4184 4450 458748545 458748284 1.230000e-85 327.0
65 TraesCS2D01G127800 chr1A 90.650 246 21 2 1859 2103 90725684 90725928 4.440000e-85 326.0
66 TraesCS2D01G127800 chr1A 82.353 187 22 6 757 937 471785396 471785215 7.970000e-33 152.0
67 TraesCS2D01G127800 chr1A 94.444 54 3 0 2102 2155 563757821 563757768 2.950000e-12 84.2
68 TraesCS2D01G127800 chr1A 97.826 46 1 0 2102 2147 527083977 527083932 3.820000e-11 80.5
69 TraesCS2D01G127800 chr1A 90.909 55 5 0 2102 2156 464796956 464796902 1.780000e-09 75.0
70 TraesCS2D01G127800 chr5D 90.323 248 22 2 1858 2104 22373850 22373604 1.600000e-84 324.0
71 TraesCS2D01G127800 chr5D 88.843 242 23 4 4184 4425 107459416 107459653 1.250000e-75 294.0
72 TraesCS2D01G127800 chr5D 98.077 52 0 1 1812 1862 52282045 52281994 6.340000e-14 89.8
73 TraesCS2D01G127800 chr5D 97.778 45 1 0 2103 2147 24098914 24098870 1.370000e-10 78.7
74 TraesCS2D01G127800 chr5D 91.379 58 3 1 2102 2159 334012260 334012205 1.370000e-10 78.7
75 TraesCS2D01G127800 chr5D 92.453 53 3 1 2102 2153 182634599 182634547 1.780000e-09 75.0
76 TraesCS2D01G127800 chrUn 89.412 255 24 3 1858 2110 452996110 452995857 7.430000e-83 318.0
77 TraesCS2D01G127800 chrUn 98.077 52 1 0 2391 2442 45102552 45102501 1.760000e-14 91.6
78 TraesCS2D01G127800 chrUn 98.077 52 1 0 2391 2442 86503864 86503915 1.760000e-14 91.6
79 TraesCS2D01G127800 chrUn 98.077 52 1 0 2391 2442 171018759 171018708 1.760000e-14 91.6
80 TraesCS2D01G127800 chrUn 98.077 52 1 0 2391 2442 186165539 186165488 1.760000e-14 91.6
81 TraesCS2D01G127800 chrUn 98.077 52 1 0 2391 2442 341859544 341859493 1.760000e-14 91.6
82 TraesCS2D01G127800 chrUn 98.077 52 1 0 2391 2442 425818309 425818258 1.760000e-14 91.6
83 TraesCS2D01G127800 chrUn 95.652 46 2 0 2102 2147 101630838 101630883 1.780000e-09 75.0
84 TraesCS2D01G127800 chrUn 95.556 45 2 0 2103 2147 362464993 362465037 6.390000e-09 73.1
85 TraesCS2D01G127800 chrUn 89.286 56 6 0 2102 2157 27476001 27475946 2.300000e-08 71.3
86 TraesCS2D01G127800 chrUn 95.455 44 2 0 2104 2147 96241790 96241833 2.300000e-08 71.3
87 TraesCS2D01G127800 chrUn 95.349 43 2 0 2105 2147 15903326 15903284 8.260000e-08 69.4
88 TraesCS2D01G127800 chrUn 97.500 40 1 0 2108 2147 28955476 28955437 8.260000e-08 69.4
89 TraesCS2D01G127800 chrUn 92.000 50 3 1 2102 2150 35125917 35125966 8.260000e-08 69.4
90 TraesCS2D01G127800 chrUn 93.478 46 3 0 2102 2147 87109159 87109204 8.260000e-08 69.4
91 TraesCS2D01G127800 chrUn 93.478 46 3 0 2102 2147 202630567 202630522 8.260000e-08 69.4
92 TraesCS2D01G127800 chrUn 91.837 49 4 0 2102 2150 349323607 349323559 8.260000e-08 69.4
93 TraesCS2D01G127800 chr4D 88.889 243 21 6 4184 4425 317117512 317117275 1.250000e-75 294.0
94 TraesCS2D01G127800 chr4D 81.046 153 15 7 4454 4594 436690889 436691039 4.870000e-20 110.0
95 TraesCS2D01G127800 chr4D 97.826 46 1 0 2102 2147 320593781 320593736 3.820000e-11 80.5
96 TraesCS2D01G127800 chr4D 97.778 45 1 0 2103 2147 64347400 64347444 1.370000e-10 78.7
97 TraesCS2D01G127800 chr4D 94.000 50 2 1 2102 2150 499776036 499775987 1.780000e-09 75.0
98 TraesCS2D01G127800 chr4D 89.130 46 5 0 683 728 15548585 15548540 1.790000e-04 58.4
99 TraesCS2D01G127800 chr4A 74.256 571 90 37 2810 3359 151642121 151642655 2.190000e-43 187.0
100 TraesCS2D01G127800 chr4A 80.303 198 28 6 734 921 635745140 635744944 6.210000e-29 139.0
101 TraesCS2D01G127800 chr4A 89.062 64 4 3 2102 2164 640236806 640236745 4.940000e-10 76.8
102 TraesCS2D01G127800 chr4A 88.679 53 6 0 683 735 585049202 585049254 1.070000e-06 65.8
103 TraesCS2D01G127800 chr4B 79.787 188 26 7 731 908 589106890 589107075 4.830000e-25 126.0
104 TraesCS2D01G127800 chr4B 94.444 54 2 1 1809 1861 180995436 180995383 1.060000e-11 82.4
105 TraesCS2D01G127800 chr4B 89.655 58 4 2 2102 2159 119340197 119340142 6.390000e-09 73.1
106 TraesCS2D01G127800 chr4B 88.525 61 6 1 2102 2161 660143380 660143320 6.390000e-09 73.1
107 TraesCS2D01G127800 chr7D 78.155 206 31 10 738 934 534625527 534625327 8.090000e-23 119.0
108 TraesCS2D01G127800 chr7D 81.046 153 15 7 4454 4594 95981707 95981857 4.870000e-20 110.0
109 TraesCS2D01G127800 chr7D 80.795 151 15 7 4456 4594 543583208 543583060 6.300000e-19 106.0
110 TraesCS2D01G127800 chr7D 91.228 57 5 0 2102 2158 87228074 87228130 1.370000e-10 78.7
111 TraesCS2D01G127800 chr1B 77.922 154 26 5 753 905 679124834 679124980 6.340000e-14 89.8
112 TraesCS2D01G127800 chr1B 85.897 78 8 2 2102 2177 282278165 282278241 3.820000e-11 80.5
113 TraesCS2D01G127800 chr1B 85.897 78 8 2 2102 2177 282278314 282278390 3.820000e-11 80.5
114 TraesCS2D01G127800 chr1B 76.316 152 33 3 739 888 587022809 587022659 1.370000e-10 78.7
115 TraesCS2D01G127800 chr7B 100.000 45 0 0 1818 1862 567598575 567598619 2.950000e-12 84.2
116 TraesCS2D01G127800 chr7B 96.078 51 1 1 1812 1862 737097879 737097928 1.060000e-11 82.4
117 TraesCS2D01G127800 chr7B 96.078 51 1 1 1812 1862 737398515 737398564 1.060000e-11 82.4
118 TraesCS2D01G127800 chr7B 96.078 51 1 1 1812 1862 737797209 737797258 1.060000e-11 82.4
119 TraesCS2D01G127800 chr7A 91.525 59 4 1 2102 2159 506684278 506684220 3.820000e-11 80.5
120 TraesCS2D01G127800 chr7A 88.060 67 7 1 2102 2168 73734890 73734825 1.370000e-10 78.7


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 TraesCS2D01G127800 chr2D 74278335 74282936 4601 True 8499.000000 8499 100.000000 1 4602 1 chr2D.!!$R1 4601
1 TraesCS2D01G127800 chr2A 73554390 73558012 3622 True 1794.333333 3101 94.194333 2 3746 3 chr2A.!!$R2 3744
2 TraesCS2D01G127800 chr2A 383426022 383426662 640 True 457.000000 457 79.971000 2686 3355 1 chr2A.!!$R1 669
3 TraesCS2D01G127800 chr2B 113323545 113327976 4431 True 1095.800000 2669 94.793000 944 4602 5 chr2B.!!$R2 3658
4 TraesCS2D01G127800 chr3B 114142387 114146282 3895 True 688.120000 1786 90.858400 371 3866 5 chr3B.!!$R3 3495
5 TraesCS2D01G127800 chr3D 67710406 67714298 3892 False 1020.000000 1550 88.611000 942 4050 3 chr3D.!!$F3 3108
6 TraesCS2D01G127800 chr3A 79400439 79404554 4115 False 596.800000 1511 90.794800 942 4045 5 chr3A.!!$F1 3103
7 TraesCS2D01G127800 chr6B 116891589 116892358 769 False 523.000000 523 79.250000 2560 3352 1 chr6B.!!$F2 792

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
290 291 0.114364 AACCTCCAACCCCCACATTC 59.886 55.0 0.0 0.0 0.00 2.67 F
475 490 0.321653 TCTTCTCCCGCTTTGCTTCC 60.322 55.0 0.0 0.0 0.00 3.46 F
1914 1988 0.104671 TGCAGCTTTTCCACTTTGGC 59.895 50.0 0.0 0.0 37.47 4.52 F
1915 1989 0.601046 GCAGCTTTTCCACTTTGGCC 60.601 55.0 0.0 0.0 37.47 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1657 1728 0.322546 GACCACAACCCAGACATCCC 60.323 60.000 0.00 0.0 0.00 3.85 R
2433 2651 0.400594 AAGGGCTTTTCGTAGGCTGT 59.599 50.000 0.00 0.0 40.34 4.40 R
3154 3434 0.740868 CCACCGTAGACATGCCTGTG 60.741 60.000 0.00 0.0 35.14 3.66 R
3774 5166 1.719780 CACGTGGTTTACTCTCTTCGC 59.280 52.381 7.95 0.0 0.00 4.70 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
27 28 7.121168 CCTCTTATACTCCTATGCTTCTCTCTG 59.879 44.444 0.00 0.00 0.00 3.35
78 79 1.737371 CGTAAGCCCGCCGTTAACA 60.737 57.895 6.39 0.00 0.00 2.41
80 81 1.737371 TAAGCCCGCCGTTAACACG 60.737 57.895 6.39 8.61 46.71 4.49
169 170 3.930336 TCTGTGCTAACCATCTTCTGTG 58.070 45.455 0.00 0.00 0.00 3.66
237 238 5.897377 AAACAATACCTCAAATCTTCCCG 57.103 39.130 0.00 0.00 0.00 5.14
247 248 2.311688 AATCTTCCCGATTCGCCGCT 62.312 55.000 0.00 0.00 37.85 5.52
290 291 0.114364 AACCTCCAACCCCCACATTC 59.886 55.000 0.00 0.00 0.00 2.67
337 338 2.602660 GCAAACACAACAACGAGCAAAT 59.397 40.909 0.00 0.00 0.00 2.32
338 339 3.301771 GCAAACACAACAACGAGCAAATC 60.302 43.478 0.00 0.00 0.00 2.17
442 444 1.079127 CCAACCGTCATCTCCGCTT 60.079 57.895 0.00 0.00 0.00 4.68
475 490 0.321653 TCTTCTCCCGCTTTGCTTCC 60.322 55.000 0.00 0.00 0.00 3.46
489 504 3.864789 TGCTTCCTCTCCTCAGTTTTT 57.135 42.857 0.00 0.00 0.00 1.94
547 586 5.690464 AAGCCTCTATCTGAATGACAAGT 57.310 39.130 0.00 0.00 0.00 3.16
568 611 4.954970 CCCAACCTGCCACACGCT 62.955 66.667 0.00 0.00 38.78 5.07
584 635 0.683412 CGCTGATCCAGATCCCATGA 59.317 55.000 5.22 0.00 37.02 3.07
625 676 1.065410 ACATGGGGTCCACCTGTCAA 61.065 55.000 0.00 0.00 35.80 3.18
754 805 1.804748 CAACCGTCAGGCCTAGTTTTC 59.195 52.381 3.98 0.00 42.76 2.29
797 848 2.560105 GTCAAAAAGCTCATCAGGCCTT 59.440 45.455 0.00 0.00 0.00 4.35
980 1039 1.790755 GATCTCTCTCTCGCTCGCTA 58.209 55.000 0.00 0.00 0.00 4.26
1025 1084 2.413765 CGGACTACCACTTCGTGTACAG 60.414 54.545 0.00 0.00 35.59 2.74
1486 1556 2.091277 GCGAGAAAGTGTCGTTCTGATG 59.909 50.000 3.07 0.00 39.69 3.07
1657 1728 3.423154 GGTTTCGCAGGCTCCACG 61.423 66.667 0.00 0.00 0.00 4.94
1749 1822 5.067283 GCCCTTCTTCTGTCAAAAACTACAA 59.933 40.000 0.00 0.00 0.00 2.41
1756 1829 8.956426 TCTTCTGTCAAAAACTACAACAAGAAT 58.044 29.630 0.00 0.00 28.71 2.40
1793 1867 7.624360 TTATGGGCATGTAAGTAGAACTTTG 57.376 36.000 0.00 0.00 39.51 2.77
1847 1921 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
1865 1939 3.447586 AGAGCGTTTAGATCACTAAGGCA 59.552 43.478 16.21 0.00 39.75 4.75
1892 1966 3.295973 TGTTTGGGCTTTTGCTTCTACT 58.704 40.909 0.00 0.00 46.54 2.57
1893 1967 3.704061 TGTTTGGGCTTTTGCTTCTACTT 59.296 39.130 0.00 0.00 46.54 2.24
1896 1970 4.320608 TGGGCTTTTGCTTCTACTTTTG 57.679 40.909 0.00 0.00 46.54 2.44
1897 1971 3.059884 GGGCTTTTGCTTCTACTTTTGC 58.940 45.455 0.00 0.00 46.54 3.68
1898 1972 3.492482 GGGCTTTTGCTTCTACTTTTGCA 60.492 43.478 0.00 0.00 46.54 4.08
1899 1973 3.737774 GGCTTTTGCTTCTACTTTTGCAG 59.262 43.478 0.00 0.00 46.54 4.41
1900 1974 3.183172 GCTTTTGCTTCTACTTTTGCAGC 59.817 43.478 0.00 0.00 43.35 5.25
1901 1975 4.614946 CTTTTGCTTCTACTTTTGCAGCT 58.385 39.130 0.00 0.00 36.75 4.24
1902 1976 4.654091 TTTGCTTCTACTTTTGCAGCTT 57.346 36.364 0.00 0.00 36.75 3.74
1903 1977 4.654091 TTGCTTCTACTTTTGCAGCTTT 57.346 36.364 0.00 0.00 36.75 3.51
1904 1978 4.654091 TGCTTCTACTTTTGCAGCTTTT 57.346 36.364 0.00 0.00 0.00 2.27
1905 1979 4.610945 TGCTTCTACTTTTGCAGCTTTTC 58.389 39.130 0.00 0.00 0.00 2.29
1906 1980 3.983988 GCTTCTACTTTTGCAGCTTTTCC 59.016 43.478 0.00 0.00 0.00 3.13
1907 1981 4.499696 GCTTCTACTTTTGCAGCTTTTCCA 60.500 41.667 0.00 0.00 0.00 3.53
1908 1982 4.568152 TCTACTTTTGCAGCTTTTCCAC 57.432 40.909 0.00 0.00 0.00 4.02
1909 1983 4.207165 TCTACTTTTGCAGCTTTTCCACT 58.793 39.130 0.00 0.00 0.00 4.00
1910 1984 3.893326 ACTTTTGCAGCTTTTCCACTT 57.107 38.095 0.00 0.00 0.00 3.16
1911 1985 4.206477 ACTTTTGCAGCTTTTCCACTTT 57.794 36.364 0.00 0.00 0.00 2.66
1912 1986 3.934579 ACTTTTGCAGCTTTTCCACTTTG 59.065 39.130 0.00 0.00 0.00 2.77
1913 1987 2.600470 TTGCAGCTTTTCCACTTTGG 57.400 45.000 0.00 0.00 39.43 3.28
1914 1988 0.104671 TGCAGCTTTTCCACTTTGGC 59.895 50.000 0.00 0.00 37.47 4.52
1915 1989 0.601046 GCAGCTTTTCCACTTTGGCC 60.601 55.000 0.00 0.00 37.47 5.36
1916 1990 0.752054 CAGCTTTTCCACTTTGGCCA 59.248 50.000 0.00 0.00 37.47 5.36
1917 1991 1.138661 CAGCTTTTCCACTTTGGCCAA 59.861 47.619 16.05 16.05 37.47 4.52
1918 1992 1.836802 AGCTTTTCCACTTTGGCCAAA 59.163 42.857 28.65 28.65 37.47 3.28
1919 1993 2.238395 AGCTTTTCCACTTTGGCCAAAA 59.762 40.909 29.93 14.05 37.47 2.44
1920 1994 3.013219 GCTTTTCCACTTTGGCCAAAAA 58.987 40.909 29.93 19.05 37.47 1.94
1921 1995 3.065233 GCTTTTCCACTTTGGCCAAAAAG 59.935 43.478 29.93 26.72 39.70 2.27
1922 1996 2.323968 TTCCACTTTGGCCAAAAAGC 57.676 45.000 29.93 0.00 40.20 3.51
1934 2008 3.002791 GCCAAAAAGCCATAAAAGCTCC 58.997 45.455 0.00 0.00 40.49 4.70
1935 2009 3.306989 GCCAAAAAGCCATAAAAGCTCCT 60.307 43.478 0.00 0.00 40.49 3.69
1936 2010 4.081697 GCCAAAAAGCCATAAAAGCTCCTA 60.082 41.667 0.00 0.00 40.49 2.94
1937 2011 5.568624 GCCAAAAAGCCATAAAAGCTCCTAA 60.569 40.000 0.00 0.00 40.49 2.69
1938 2012 6.463360 CCAAAAAGCCATAAAAGCTCCTAAA 58.537 36.000 0.00 0.00 40.49 1.85
1939 2013 7.105588 CCAAAAAGCCATAAAAGCTCCTAAAT 58.894 34.615 0.00 0.00 40.49 1.40
1940 2014 8.257306 CCAAAAAGCCATAAAAGCTCCTAAATA 58.743 33.333 0.00 0.00 40.49 1.40
1941 2015 9.305925 CAAAAAGCCATAAAAGCTCCTAAATAG 57.694 33.333 0.00 0.00 40.49 1.73
1942 2016 7.588497 AAAGCCATAAAAGCTCCTAAATAGG 57.412 36.000 0.00 0.00 40.49 2.57
1943 2017 6.267492 AGCCATAAAAGCTCCTAAATAGGT 57.733 37.500 6.39 0.00 44.02 3.08
1944 2018 6.064717 AGCCATAAAAGCTCCTAAATAGGTG 58.935 40.000 6.39 5.41 44.02 4.00
1954 2028 5.501156 CTCCTAAATAGGTGCTTTTGGAGT 58.499 41.667 13.89 0.00 44.04 3.85
1955 2029 5.887754 TCCTAAATAGGTGCTTTTGGAGTT 58.112 37.500 6.39 0.00 44.02 3.01
1956 2030 6.311735 TCCTAAATAGGTGCTTTTGGAGTTT 58.688 36.000 6.39 0.00 44.02 2.66
1957 2031 6.780522 TCCTAAATAGGTGCTTTTGGAGTTTT 59.219 34.615 6.39 0.00 44.02 2.43
1958 2032 7.039993 TCCTAAATAGGTGCTTTTGGAGTTTTC 60.040 37.037 6.39 0.00 44.02 2.29
1959 2033 6.478512 AAATAGGTGCTTTTGGAGTTTTCA 57.521 33.333 0.00 0.00 0.00 2.69
1960 2034 6.670695 AATAGGTGCTTTTGGAGTTTTCAT 57.329 33.333 0.00 0.00 0.00 2.57
1961 2035 4.326504 AGGTGCTTTTGGAGTTTTCATG 57.673 40.909 0.00 0.00 0.00 3.07
1962 2036 3.070015 AGGTGCTTTTGGAGTTTTCATGG 59.930 43.478 0.00 0.00 0.00 3.66
1963 2037 2.802247 GTGCTTTTGGAGTTTTCATGGC 59.198 45.455 0.00 0.00 0.00 4.40
1964 2038 2.699846 TGCTTTTGGAGTTTTCATGGCT 59.300 40.909 0.00 0.00 0.00 4.75
1965 2039 3.134442 TGCTTTTGGAGTTTTCATGGCTT 59.866 39.130 0.00 0.00 0.00 4.35
1966 2040 4.129380 GCTTTTGGAGTTTTCATGGCTTT 58.871 39.130 0.00 0.00 0.00 3.51
1967 2041 4.576053 GCTTTTGGAGTTTTCATGGCTTTT 59.424 37.500 0.00 0.00 0.00 2.27
1968 2042 5.277490 GCTTTTGGAGTTTTCATGGCTTTTC 60.277 40.000 0.00 0.00 0.00 2.29
1969 2043 3.641437 TGGAGTTTTCATGGCTTTTCG 57.359 42.857 0.00 0.00 0.00 3.46
1970 2044 3.218453 TGGAGTTTTCATGGCTTTTCGA 58.782 40.909 0.00 0.00 0.00 3.71
1971 2045 3.253188 TGGAGTTTTCATGGCTTTTCGAG 59.747 43.478 0.00 0.00 0.00 4.04
1983 2057 3.774066 GCTTTTCGAGCCAAATATTGCT 58.226 40.909 0.12 0.12 46.01 3.91
1984 2058 4.920376 GCTTTTCGAGCCAAATATTGCTA 58.080 39.130 0.55 0.00 46.01 3.49
1985 2059 4.972440 GCTTTTCGAGCCAAATATTGCTAG 59.028 41.667 0.55 1.69 46.01 3.42
1986 2060 5.220854 GCTTTTCGAGCCAAATATTGCTAGA 60.221 40.000 6.52 6.52 46.01 2.43
1987 2061 6.514048 GCTTTTCGAGCCAAATATTGCTAGAT 60.514 38.462 10.13 0.00 46.01 1.98
1988 2062 6.942532 TTTCGAGCCAAATATTGCTAGATT 57.057 33.333 10.13 0.00 38.68 2.40
1989 2063 5.929697 TCGAGCCAAATATTGCTAGATTG 57.070 39.130 6.52 0.00 38.11 2.67
1990 2064 5.610398 TCGAGCCAAATATTGCTAGATTGA 58.390 37.500 6.52 0.00 38.11 2.57
1991 2065 6.233434 TCGAGCCAAATATTGCTAGATTGAT 58.767 36.000 6.52 0.00 38.11 2.57
1992 2066 6.712095 TCGAGCCAAATATTGCTAGATTGATT 59.288 34.615 6.52 0.00 38.11 2.57
1993 2067 7.020010 CGAGCCAAATATTGCTAGATTGATTC 58.980 38.462 0.00 0.00 38.11 2.52
1994 2068 7.308169 CGAGCCAAATATTGCTAGATTGATTCA 60.308 37.037 0.00 0.00 38.11 2.57
1995 2069 8.418597 AGCCAAATATTGCTAGATTGATTCAT 57.581 30.769 0.00 0.00 35.69 2.57
1996 2070 8.304596 AGCCAAATATTGCTAGATTGATTCATG 58.695 33.333 0.00 0.00 35.69 3.07
1997 2071 8.301720 GCCAAATATTGCTAGATTGATTCATGA 58.698 33.333 0.00 0.00 0.00 3.07
2002 2076 9.909644 ATATTGCTAGATTGATTCATGAAAAGC 57.090 29.630 13.09 6.12 0.00 3.51
2003 2077 6.140303 TGCTAGATTGATTCATGAAAAGCC 57.860 37.500 13.09 3.17 0.00 4.35
2004 2078 5.653330 TGCTAGATTGATTCATGAAAAGCCA 59.347 36.000 13.09 5.74 0.00 4.75
2005 2079 6.322969 TGCTAGATTGATTCATGAAAAGCCAT 59.677 34.615 13.09 2.75 0.00 4.40
2006 2080 7.503230 TGCTAGATTGATTCATGAAAAGCCATA 59.497 33.333 13.09 1.92 0.00 2.74
2007 2081 8.355169 GCTAGATTGATTCATGAAAAGCCATAA 58.645 33.333 13.09 1.20 0.00 1.90
2010 2084 9.374838 AGATTGATTCATGAAAAGCCATAAAAC 57.625 29.630 13.09 0.00 0.00 2.43
2011 2085 9.374838 GATTGATTCATGAAAAGCCATAAAACT 57.625 29.630 13.09 0.00 0.00 2.66
2012 2086 8.761575 TTGATTCATGAAAAGCCATAAAACTC 57.238 30.769 13.09 1.18 0.00 3.01
2013 2087 7.322664 TGATTCATGAAAAGCCATAAAACTCC 58.677 34.615 13.09 0.00 0.00 3.85
2014 2088 6.662865 TTCATGAAAAGCCATAAAACTCCA 57.337 33.333 5.45 0.00 0.00 3.86
2015 2089 6.662865 TCATGAAAAGCCATAAAACTCCAA 57.337 33.333 0.00 0.00 0.00 3.53
2016 2090 7.060383 TCATGAAAAGCCATAAAACTCCAAA 57.940 32.000 0.00 0.00 0.00 3.28
2017 2091 7.504403 TCATGAAAAGCCATAAAACTCCAAAA 58.496 30.769 0.00 0.00 0.00 2.44
2018 2092 7.656948 TCATGAAAAGCCATAAAACTCCAAAAG 59.343 33.333 0.00 0.00 0.00 2.27
2019 2093 5.757808 TGAAAAGCCATAAAACTCCAAAAGC 59.242 36.000 0.00 0.00 0.00 3.51
2020 2094 4.953940 AAGCCATAAAACTCCAAAAGCA 57.046 36.364 0.00 0.00 0.00 3.91
2021 2095 4.953940 AGCCATAAAACTCCAAAAGCAA 57.046 36.364 0.00 0.00 0.00 3.91
2022 2096 4.631131 AGCCATAAAACTCCAAAAGCAAC 58.369 39.130 0.00 0.00 0.00 4.17
2023 2097 4.344968 AGCCATAAAACTCCAAAAGCAACT 59.655 37.500 0.00 0.00 0.00 3.16
2024 2098 5.538433 AGCCATAAAACTCCAAAAGCAACTA 59.462 36.000 0.00 0.00 0.00 2.24
2025 2099 6.211384 AGCCATAAAACTCCAAAAGCAACTAT 59.789 34.615 0.00 0.00 0.00 2.12
2026 2100 6.873605 GCCATAAAACTCCAAAAGCAACTATT 59.126 34.615 0.00 0.00 0.00 1.73
2027 2101 7.387673 GCCATAAAACTCCAAAAGCAACTATTT 59.612 33.333 0.00 0.00 0.00 1.40
2028 2102 9.921637 CCATAAAACTCCAAAAGCAACTATTTA 57.078 29.630 0.00 0.00 0.00 1.40
2123 2197 6.425417 GGCCTAAAGTAGTGATCTAAATGCTC 59.575 42.308 0.00 0.00 0.00 4.26
2167 2241 9.535878 GGGAGTGTTTGTTATGTTGATTAAAAA 57.464 29.630 0.00 0.00 0.00 1.94
2344 2449 7.624549 AGATAACCATACCACACCATGATATC 58.375 38.462 0.00 0.00 0.00 1.63
2370 2475 6.512342 TCCTCTTCTTTTCTAGTACTTCGG 57.488 41.667 0.00 0.00 0.00 4.30
2380 2598 7.472334 TTTCTAGTACTTCGGTTTACTCCAT 57.528 36.000 0.00 0.00 0.00 3.41
2384 2602 3.515330 ACTTCGGTTTACTCCATACGG 57.485 47.619 0.00 0.00 0.00 4.02
3012 3234 4.159693 AGTGAACAGTGTGCGATATTAGGA 59.840 41.667 0.00 0.00 0.00 2.94
3013 3235 5.050490 GTGAACAGTGTGCGATATTAGGAT 58.950 41.667 0.00 0.00 0.00 3.24
3051 3322 3.308053 CAGTCGCAGGATACAATTCACAG 59.692 47.826 0.00 0.00 41.41 3.66
3115 3394 3.914426 TCTTTGACCTTAGGATGAGGC 57.086 47.619 4.77 0.00 37.84 4.70
3154 3434 8.738645 ACTAAGAGGAAATCATGTTCATTACC 57.261 34.615 0.00 0.00 0.00 2.85
3180 3463 4.777896 AGGCATGTCTACGGTGGATATATT 59.222 41.667 0.00 0.00 0.00 1.28
3333 3622 7.671827 CGAATATGTCGTGTGAATAAGAAACA 58.328 34.615 0.00 0.00 45.09 2.83
3396 3695 6.128553 ACACGTAATCTTTAAGTGTCATGCAG 60.129 38.462 11.49 0.00 41.55 4.41
3406 3705 0.994247 TGTCATGCAGGGTCTTCCAT 59.006 50.000 0.00 0.00 38.24 3.41
3746 4047 6.074195 TGTTTTGACGAGGTTCTGTATAAACG 60.074 38.462 0.00 0.00 30.35 3.60
3774 5166 8.765044 TTTGCGAAAATTTAAGCAATTTGAAG 57.235 26.923 24.39 0.00 46.92 3.02
3916 6816 0.037326 GTGTGCCTGTCTTCCATCGA 60.037 55.000 0.00 0.00 0.00 3.59
3963 6881 2.370445 CCCTGCCTGAATCCCGTCT 61.370 63.158 0.00 0.00 0.00 4.18
4041 6959 3.878667 GGCGAATCCCCCTCCAGG 61.879 72.222 0.00 0.00 0.00 4.45
4063 7042 4.359706 GTTCGAGGCATGAACTTTGTTTT 58.640 39.130 12.80 0.00 41.89 2.43
4108 7094 1.200948 GCAACTTGTGATTGGGCTCTC 59.799 52.381 0.00 0.00 0.00 3.20
4189 7175 2.368875 GCCGATCCCTTTCTAATGAGGA 59.631 50.000 0.00 0.00 34.91 3.71
4199 7185 4.503714 TTCTAATGAGGACATCCCAACC 57.496 45.455 0.00 0.00 35.50 3.77
4217 7203 0.690192 CCATGGACACTACACCACCA 59.310 55.000 5.56 0.00 39.06 4.17
4223 7209 3.270877 GGACACTACACCACCAATCATC 58.729 50.000 0.00 0.00 0.00 2.92
4240 7226 2.749076 TCATCAAAGGTCCAATCGCAAG 59.251 45.455 0.00 0.00 0.00 4.01
4254 7240 1.654220 GCAAGAAGCCGTGCAAAGA 59.346 52.632 0.00 0.00 45.19 2.52
4314 7300 7.353414 TCATTTGACCTTGAAAACATGGTTA 57.647 32.000 0.00 3.28 33.45 2.85
4340 7326 2.036387 TCACCTCTCCTTCGTTGTTGA 58.964 47.619 0.00 0.00 0.00 3.18
4388 7374 5.505173 AGACCAACAACATTTTCAGTCAG 57.495 39.130 0.00 0.00 0.00 3.51
4426 7412 8.816144 TGTTTTATGATGAAGAAACAAAGTTGC 58.184 29.630 0.00 0.00 38.58 4.17
4452 7438 7.148787 CGAAGAAATAGGTTGTCTACTGAACAC 60.149 40.741 0.00 0.00 0.00 3.32
4492 7478 4.497473 TTTTCAGTCCGTGCCAAAATAG 57.503 40.909 0.00 0.00 0.00 1.73
4553 7539 7.506114 AGGTTGTCTACTGAAGAAACATTGTA 58.494 34.615 0.00 0.00 35.47 2.41
4554 7540 7.990886 AGGTTGTCTACTGAAGAAACATTGTAA 59.009 33.333 0.00 0.00 35.47 2.41
4559 7545 9.151471 GTCTACTGAAGAAACATTGTAATAGCA 57.849 33.333 0.00 0.00 35.47 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.252995 AGAGAAGCATAGGAGTATAAGAGGG 58.747 44.000 0.00 0.00 0.00 4.30
7 8 8.584157 CAATTACAGAGAGAAGCATAGGAGTAT 58.416 37.037 0.00 0.00 0.00 2.12
15 16 6.428159 ACGAAAACAATTACAGAGAGAAGCAT 59.572 34.615 0.00 0.00 0.00 3.79
19 20 7.042051 CCAAGACGAAAACAATTACAGAGAGAA 60.042 37.037 0.00 0.00 0.00 2.87
96 97 9.520515 AAGGAATATTCAAAGTAAGAGCAAAGA 57.479 29.630 17.07 0.00 0.00 2.52
130 131 8.976986 AGCACAGAATTATTCAAAAACAGATC 57.023 30.769 7.74 0.00 0.00 2.75
212 213 6.598064 CGGGAAGATTTGAGGTATTGTTTACT 59.402 38.462 0.00 0.00 0.00 2.24
290 291 6.430451 GCTCGAGATATATTTTTGTTGGTGG 58.570 40.000 18.75 0.00 0.00 4.61
337 338 0.972983 CTTGCCCTCTTCTCCTCCGA 60.973 60.000 0.00 0.00 0.00 4.55
338 339 1.519719 CTTGCCCTCTTCTCCTCCG 59.480 63.158 0.00 0.00 0.00 4.63
339 340 1.631071 CCCTTGCCCTCTTCTCCTCC 61.631 65.000 0.00 0.00 0.00 4.30
340 341 1.911471 CCCTTGCCCTCTTCTCCTC 59.089 63.158 0.00 0.00 0.00 3.71
475 490 3.312421 TGCGAAACAAAAACTGAGGAGAG 59.688 43.478 0.00 0.00 0.00 3.20
489 504 0.310543 GTGCCACTGATTGCGAAACA 59.689 50.000 0.00 0.00 0.00 2.83
568 611 0.683412 CGCTCATGGGATCTGGATCA 59.317 55.000 11.93 0.00 39.54 2.92
608 659 1.767692 GTTGACAGGTGGACCCCAT 59.232 57.895 2.29 0.00 35.28 4.00
625 676 2.593026 GAGAGAATGGGAGAGATCGGT 58.407 52.381 0.00 0.00 0.00 4.69
741 792 3.905249 GCCGGAAAACTAGGCCTG 58.095 61.111 17.99 8.18 44.80 4.85
797 848 0.619255 TAAGAATGAGGCCCGACCCA 60.619 55.000 0.00 0.00 40.58 4.51
810 861 8.720562 GGCTTGTTGTATTTGCAATTTAAGAAT 58.279 29.630 0.00 0.00 0.00 2.40
856 907 1.536709 GCCTAGATTTTGCGCCCAATG 60.537 52.381 4.18 0.00 0.00 2.82
857 908 0.746659 GCCTAGATTTTGCGCCCAAT 59.253 50.000 4.18 2.26 0.00 3.16
858 909 1.319614 GGCCTAGATTTTGCGCCCAA 61.320 55.000 4.18 0.00 33.30 4.12
859 910 1.752694 GGCCTAGATTTTGCGCCCA 60.753 57.895 4.18 0.00 33.30 5.36
860 911 3.120105 GGCCTAGATTTTGCGCCC 58.880 61.111 4.18 0.00 33.30 6.13
864 915 2.119009 GGCTGGGCCTAGATTTTGC 58.881 57.895 22.15 3.40 46.69 3.68
980 1039 3.816524 CCGAGCCTCGAACGAGCT 61.817 66.667 17.19 16.61 43.74 4.09
1486 1556 3.196040 TGGATTTCTGGCTCCATGC 57.804 52.632 0.00 0.00 36.63 4.06
1657 1728 0.322546 GACCACAACCCAGACATCCC 60.323 60.000 0.00 0.00 0.00 3.85
1708 1779 9.520515 GAAGAAGGGCATCATATTAAATAGGAA 57.479 33.333 0.00 0.00 0.00 3.36
1847 1921 4.495422 ACAGTGCCTTAGTGATCTAAACG 58.505 43.478 0.00 0.00 35.98 3.60
1865 1939 2.027285 AGCAAAAGCCCAAACAAACAGT 60.027 40.909 0.00 0.00 0.00 3.55
1892 1966 3.269178 CCAAAGTGGAAAAGCTGCAAAA 58.731 40.909 1.02 0.00 40.96 2.44
1893 1967 2.903798 CCAAAGTGGAAAAGCTGCAAA 58.096 42.857 1.02 0.00 40.96 3.68
1896 1970 0.601046 GGCCAAAGTGGAAAAGCTGC 60.601 55.000 0.00 0.00 40.96 5.25
1897 1971 0.752054 TGGCCAAAGTGGAAAAGCTG 59.248 50.000 0.61 0.00 40.96 4.24
1898 1972 1.494960 TTGGCCAAAGTGGAAAAGCT 58.505 45.000 17.98 0.00 40.96 3.74
1899 1973 2.323968 TTTGGCCAAAGTGGAAAAGC 57.676 45.000 27.13 0.00 40.96 3.51
1900 1974 3.065233 GCTTTTTGGCCAAAGTGGAAAAG 59.935 43.478 28.79 26.24 40.96 2.27
1901 1975 3.013219 GCTTTTTGGCCAAAGTGGAAAA 58.987 40.909 28.79 18.57 40.96 2.29
1902 1976 2.637947 GCTTTTTGGCCAAAGTGGAAA 58.362 42.857 28.79 19.24 40.96 3.13
1903 1977 2.323968 GCTTTTTGGCCAAAGTGGAA 57.676 45.000 28.79 19.58 40.96 3.53
1913 1987 3.002791 GGAGCTTTTATGGCTTTTTGGC 58.997 45.455 0.00 0.00 40.40 4.52
1914 1988 4.541973 AGGAGCTTTTATGGCTTTTTGG 57.458 40.909 0.00 0.00 40.40 3.28
1915 1989 9.305925 CTATTTAGGAGCTTTTATGGCTTTTTG 57.694 33.333 0.00 0.00 40.40 2.44
1916 1990 8.478066 CCTATTTAGGAGCTTTTATGGCTTTTT 58.522 33.333 0.00 0.00 46.63 1.94
1917 1991 7.619698 ACCTATTTAGGAGCTTTTATGGCTTTT 59.380 33.333 10.61 0.00 46.63 2.27
1918 1992 7.068716 CACCTATTTAGGAGCTTTTATGGCTTT 59.931 37.037 10.61 0.00 46.63 3.51
1919 1993 6.547510 CACCTATTTAGGAGCTTTTATGGCTT 59.452 38.462 10.61 0.00 46.63 4.35
1920 1994 6.064717 CACCTATTTAGGAGCTTTTATGGCT 58.935 40.000 10.61 0.00 46.63 4.75
1921 1995 6.319141 CACCTATTTAGGAGCTTTTATGGC 57.681 41.667 10.61 0.00 46.63 4.40
1931 2005 5.501156 ACTCCAAAAGCACCTATTTAGGAG 58.499 41.667 10.61 0.00 46.63 3.69
1932 2006 5.514500 ACTCCAAAAGCACCTATTTAGGA 57.486 39.130 10.61 0.00 46.63 2.94
1934 2008 7.657336 TGAAAACTCCAAAAGCACCTATTTAG 58.343 34.615 0.00 0.00 0.00 1.85
1935 2009 7.589958 TGAAAACTCCAAAAGCACCTATTTA 57.410 32.000 0.00 0.00 0.00 1.40
1936 2010 6.478512 TGAAAACTCCAAAAGCACCTATTT 57.521 33.333 0.00 0.00 0.00 1.40
1937 2011 6.458210 CATGAAAACTCCAAAAGCACCTATT 58.542 36.000 0.00 0.00 0.00 1.73
1938 2012 5.047092 CCATGAAAACTCCAAAAGCACCTAT 60.047 40.000 0.00 0.00 0.00 2.57
1939 2013 4.280677 CCATGAAAACTCCAAAAGCACCTA 59.719 41.667 0.00 0.00 0.00 3.08
1940 2014 3.070015 CCATGAAAACTCCAAAAGCACCT 59.930 43.478 0.00 0.00 0.00 4.00
1941 2015 3.392882 CCATGAAAACTCCAAAAGCACC 58.607 45.455 0.00 0.00 0.00 5.01
1942 2016 2.802247 GCCATGAAAACTCCAAAAGCAC 59.198 45.455 0.00 0.00 0.00 4.40
1943 2017 2.699846 AGCCATGAAAACTCCAAAAGCA 59.300 40.909 0.00 0.00 0.00 3.91
1944 2018 3.391506 AGCCATGAAAACTCCAAAAGC 57.608 42.857 0.00 0.00 0.00 3.51
1945 2019 5.050837 CGAAAAGCCATGAAAACTCCAAAAG 60.051 40.000 0.00 0.00 0.00 2.27
1946 2020 4.808364 CGAAAAGCCATGAAAACTCCAAAA 59.192 37.500 0.00 0.00 0.00 2.44
1947 2021 4.098654 TCGAAAAGCCATGAAAACTCCAAA 59.901 37.500 0.00 0.00 0.00 3.28
1948 2022 3.634448 TCGAAAAGCCATGAAAACTCCAA 59.366 39.130 0.00 0.00 0.00 3.53
1949 2023 3.218453 TCGAAAAGCCATGAAAACTCCA 58.782 40.909 0.00 0.00 0.00 3.86
1950 2024 3.826466 CTCGAAAAGCCATGAAAACTCC 58.174 45.455 0.00 0.00 0.00 3.85
1951 2025 3.237628 GCTCGAAAAGCCATGAAAACTC 58.762 45.455 0.00 0.00 45.92 3.01
1952 2026 3.288809 GCTCGAAAAGCCATGAAAACT 57.711 42.857 0.00 0.00 45.92 2.66
1963 2037 6.363577 TCTAGCAATATTTGGCTCGAAAAG 57.636 37.500 3.70 0.00 41.41 2.27
1964 2038 6.942532 ATCTAGCAATATTTGGCTCGAAAA 57.057 33.333 3.70 0.00 41.41 2.29
1965 2039 6.542005 TCAATCTAGCAATATTTGGCTCGAAA 59.458 34.615 3.70 0.00 41.41 3.46
1966 2040 6.054941 TCAATCTAGCAATATTTGGCTCGAA 58.945 36.000 3.70 0.00 41.41 3.71
1967 2041 5.610398 TCAATCTAGCAATATTTGGCTCGA 58.390 37.500 3.70 4.41 41.41 4.04
1968 2042 5.929697 TCAATCTAGCAATATTTGGCTCG 57.070 39.130 3.70 0.00 41.41 5.03
1969 2043 7.879070 TGAATCAATCTAGCAATATTTGGCTC 58.121 34.615 3.70 0.00 41.41 4.70
1970 2044 7.828508 TGAATCAATCTAGCAATATTTGGCT 57.171 32.000 5.68 5.68 43.94 4.75
1971 2045 8.301720 TCATGAATCAATCTAGCAATATTTGGC 58.698 33.333 0.00 0.00 0.00 4.52
1976 2050 9.909644 GCTTTTCATGAATCAATCTAGCAATAT 57.090 29.630 9.40 0.00 0.00 1.28
1977 2051 8.355169 GGCTTTTCATGAATCAATCTAGCAATA 58.645 33.333 9.40 0.00 0.00 1.90
1978 2052 7.147794 TGGCTTTTCATGAATCAATCTAGCAAT 60.148 33.333 9.40 0.00 0.00 3.56
1979 2053 6.153170 TGGCTTTTCATGAATCAATCTAGCAA 59.847 34.615 9.40 1.48 0.00 3.91
1980 2054 5.653330 TGGCTTTTCATGAATCAATCTAGCA 59.347 36.000 9.40 0.00 0.00 3.49
1981 2055 6.140303 TGGCTTTTCATGAATCAATCTAGC 57.860 37.500 9.40 9.24 0.00 3.42
1984 2058 9.374838 GTTTTATGGCTTTTCATGAATCAATCT 57.625 29.630 9.40 0.00 0.00 2.40
1985 2059 9.374838 AGTTTTATGGCTTTTCATGAATCAATC 57.625 29.630 9.40 0.00 0.00 2.67
1986 2060 9.374838 GAGTTTTATGGCTTTTCATGAATCAAT 57.625 29.630 9.40 3.82 0.00 2.57
1987 2061 7.818930 GGAGTTTTATGGCTTTTCATGAATCAA 59.181 33.333 9.40 0.42 0.00 2.57
1988 2062 7.039152 TGGAGTTTTATGGCTTTTCATGAATCA 60.039 33.333 9.40 6.39 0.00 2.57
1989 2063 7.322664 TGGAGTTTTATGGCTTTTCATGAATC 58.677 34.615 9.40 1.85 0.00 2.52
1990 2064 7.243604 TGGAGTTTTATGGCTTTTCATGAAT 57.756 32.000 9.40 0.00 0.00 2.57
1991 2065 6.662865 TGGAGTTTTATGGCTTTTCATGAA 57.337 33.333 3.38 3.38 0.00 2.57
1992 2066 6.662865 TTGGAGTTTTATGGCTTTTCATGA 57.337 33.333 0.00 0.00 0.00 3.07
1993 2067 7.571798 GCTTTTGGAGTTTTATGGCTTTTCATG 60.572 37.037 0.00 0.00 0.00 3.07
1994 2068 6.427853 GCTTTTGGAGTTTTATGGCTTTTCAT 59.572 34.615 0.00 0.00 0.00 2.57
1995 2069 5.757808 GCTTTTGGAGTTTTATGGCTTTTCA 59.242 36.000 0.00 0.00 0.00 2.69
1996 2070 5.757808 TGCTTTTGGAGTTTTATGGCTTTTC 59.242 36.000 0.00 0.00 0.00 2.29
1997 2071 5.679601 TGCTTTTGGAGTTTTATGGCTTTT 58.320 33.333 0.00 0.00 0.00 2.27
1998 2072 5.289083 TGCTTTTGGAGTTTTATGGCTTT 57.711 34.783 0.00 0.00 0.00 3.51
1999 2073 4.953940 TGCTTTTGGAGTTTTATGGCTT 57.046 36.364 0.00 0.00 0.00 4.35
2000 2074 4.344968 AGTTGCTTTTGGAGTTTTATGGCT 59.655 37.500 0.00 0.00 0.00 4.75
2001 2075 4.631131 AGTTGCTTTTGGAGTTTTATGGC 58.369 39.130 0.00 0.00 0.00 4.40
2002 2076 8.831715 AAATAGTTGCTTTTGGAGTTTTATGG 57.168 30.769 0.00 0.00 0.00 2.74
2007 2081 9.914131 GATTCTAAATAGTTGCTTTTGGAGTTT 57.086 29.630 0.00 0.00 0.00 2.66
2008 2082 9.301897 AGATTCTAAATAGTTGCTTTTGGAGTT 57.698 29.630 0.00 0.00 0.00 3.01
2009 2083 8.870075 AGATTCTAAATAGTTGCTTTTGGAGT 57.130 30.769 0.00 0.00 0.00 3.85
2017 2091 9.413734 AGCCATAAAAGATTCTAAATAGTTGCT 57.586 29.630 0.00 0.00 0.00 3.91
2025 2099 9.705290 GACCAAAAAGCCATAAAAGATTCTAAA 57.295 29.630 0.00 0.00 0.00 1.85
2026 2100 8.865090 TGACCAAAAAGCCATAAAAGATTCTAA 58.135 29.630 0.00 0.00 0.00 2.10
2027 2101 8.415950 TGACCAAAAAGCCATAAAAGATTCTA 57.584 30.769 0.00 0.00 0.00 2.10
2028 2102 7.301868 TGACCAAAAAGCCATAAAAGATTCT 57.698 32.000 0.00 0.00 0.00 2.40
2029 2103 7.961325 TTGACCAAAAAGCCATAAAAGATTC 57.039 32.000 0.00 0.00 0.00 2.52
2030 2104 7.992608 ACTTTGACCAAAAAGCCATAAAAGATT 59.007 29.630 0.00 0.00 40.20 2.40
2031 2105 7.442062 CACTTTGACCAAAAAGCCATAAAAGAT 59.558 33.333 0.00 0.00 40.20 2.40
2032 2106 6.760770 CACTTTGACCAAAAAGCCATAAAAGA 59.239 34.615 0.00 0.00 40.20 2.52
2050 2124 3.815856 TTTGCAGCATTTCCACTTTGA 57.184 38.095 0.00 0.00 0.00 2.69
2123 2197 6.761714 ACACTCCCGCTGTAAAGAAATATAAG 59.238 38.462 0.00 0.00 0.00 1.73
2257 2332 2.519013 AGGTCAGATTTTGCCAGAACC 58.481 47.619 0.00 0.00 0.00 3.62
2344 2449 7.542824 CCGAAGTACTAGAAAAGAAGAGGAAAG 59.457 40.741 0.00 0.00 0.00 2.62
2362 2467 4.142381 ACCGTATGGAGTAAACCGAAGTAC 60.142 45.833 8.33 0.00 39.21 2.73
2363 2468 4.016444 ACCGTATGGAGTAAACCGAAGTA 58.984 43.478 8.33 0.00 39.21 2.24
2364 2469 2.827921 ACCGTATGGAGTAAACCGAAGT 59.172 45.455 8.33 0.00 39.21 3.01
2370 2475 3.075866 CGGAGACCGTATGGAGTAAAC 57.924 52.381 8.33 0.00 42.73 2.01
2384 2602 0.868406 CCTGTTCTGTTTGCGGAGAC 59.132 55.000 0.00 0.00 0.00 3.36
2433 2651 0.400594 AAGGGCTTTTCGTAGGCTGT 59.599 50.000 0.00 0.00 40.34 4.40
2889 3108 7.593825 ACTTGAACTAACATAATGGAAACTGC 58.406 34.615 0.00 0.00 0.00 4.40
3012 3234 5.356751 TGCGACTGGCTAATTGAAACATAAT 59.643 36.000 0.00 0.00 44.05 1.28
3013 3235 4.697828 TGCGACTGGCTAATTGAAACATAA 59.302 37.500 0.00 0.00 44.05 1.90
3115 3394 6.034161 TCCTCTTAGTACGGAAGGAAAAAG 57.966 41.667 9.77 1.78 0.00 2.27
3154 3434 0.740868 CCACCGTAGACATGCCTGTG 60.741 60.000 0.00 0.00 35.14 3.66
3180 3463 3.719268 AGGCAAACATACATCAGGACA 57.281 42.857 0.00 0.00 0.00 4.02
3246 3535 3.733337 CCACTGTATTAGGCACTCATCC 58.267 50.000 0.00 0.00 41.75 3.51
3333 3622 4.401202 AGTGGTCAAGAAAAATCCGTTGTT 59.599 37.500 0.00 0.00 0.00 2.83
3396 3695 5.760743 GTCTAGCATAAAGAATGGAAGACCC 59.239 44.000 0.00 0.00 35.99 4.46
3406 3705 9.507329 AACAGAATGAAAGTCTAGCATAAAGAA 57.493 29.630 0.00 0.00 40.65 2.52
3467 3766 4.358214 TGTCCATCATTCAGTACTGGGTA 58.642 43.478 22.48 9.10 0.00 3.69
3746 4047 8.061268 TCAAATTGCTTAAATTTTCGCAAAGTC 58.939 29.630 22.36 7.55 44.41 3.01
3774 5166 1.719780 CACGTGGTTTACTCTCTTCGC 59.280 52.381 7.95 0.00 0.00 4.70
3916 6816 2.828877 TCAAGAACAAATCGTCACCGT 58.171 42.857 0.00 0.00 35.01 4.83
3963 6881 2.042230 GGGGAGTAGGGAAGCGGA 60.042 66.667 0.00 0.00 0.00 5.54
4041 6959 3.626028 AACAAAGTTCATGCCTCGAAC 57.374 42.857 0.00 0.00 42.52 3.95
4082 7061 2.118683 CCAATCACAAGTTGCAACACG 58.881 47.619 30.11 21.83 0.00 4.49
4108 7094 5.466819 TGTACTCTACCATTTGTGAAGTCG 58.533 41.667 0.00 0.00 0.00 4.18
4151 7137 1.001378 CGGCAATTTGCTACTATGGCC 60.001 52.381 20.06 0.00 44.28 5.36
4155 7141 3.073062 AGGGATCGGCAATTTGCTACTAT 59.927 43.478 20.06 9.10 44.28 2.12
4189 7175 1.075601 AGTGTCCATGGTTGGGATGT 58.924 50.000 12.58 0.00 43.81 3.06
4199 7185 2.559698 TTGGTGGTGTAGTGTCCATG 57.440 50.000 0.00 0.00 36.09 3.66
4217 7203 3.355378 TGCGATTGGACCTTTGATGATT 58.645 40.909 0.00 0.00 0.00 2.57
4223 7209 2.669391 GCTTCTTGCGATTGGACCTTTG 60.669 50.000 0.00 0.00 0.00 2.77
4240 7226 3.896122 TGTATTTTCTTTGCACGGCTTC 58.104 40.909 0.00 0.00 0.00 3.86
4244 7230 5.639757 TGATCATGTATTTTCTTTGCACGG 58.360 37.500 0.00 0.00 0.00 4.94
4254 7240 4.943705 AGCGTTCACCTGATCATGTATTTT 59.056 37.500 3.11 0.00 0.00 1.82
4314 7300 0.539051 CGAAGGAGAGGTGAAGGCAT 59.461 55.000 0.00 0.00 0.00 4.40
4340 7326 2.485426 CGATGTTGCACCTGAGTTCAAT 59.515 45.455 0.00 0.00 31.72 2.57
4388 7374 8.755696 TTCATCATAAAACACTATTTTGGCAC 57.244 30.769 0.00 0.00 0.00 5.01
4418 7404 5.519722 ACAACCTATTTCTTCGCAACTTTG 58.480 37.500 0.00 0.00 0.00 2.77
4426 7412 6.866770 TGTTCAGTAGACAACCTATTTCTTCG 59.133 38.462 0.00 0.00 0.00 3.79
4452 7438 4.568152 AAATGTTGTTGGTCTTCTTCGG 57.432 40.909 0.00 0.00 0.00 4.30
4518 7504 5.408356 TCAGTAGACAACCTATTTCTTCGC 58.592 41.667 0.00 0.00 0.00 4.70
4553 7539 6.346758 CGTGCAAAACATTGTTTCATGCTATT 60.347 34.615 26.84 6.72 33.66 1.73
4554 7540 5.118971 CGTGCAAAACATTGTTTCATGCTAT 59.881 36.000 26.84 7.30 33.66 2.97
4559 7545 4.681744 ACTCGTGCAAAACATTGTTTCAT 58.318 34.783 14.80 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.