Multiple sequence alignment - TraesCS1D01G021100

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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 TraesCS1D01G021100 chr1D 100.000 6172 0 0 1 6172 9053727 9059898 0.000000e+00 11398.0
1 TraesCS1D01G021100 chr1D 86.780 295 34 5 3558 3848 9482999 9482706 2.150000e-84 324.0
2 TraesCS1D01G021100 chr1D 85.965 171 21 3 2896 3064 31680766 31680597 4.920000e-41 180.0
3 TraesCS1D01G021100 chr1D 85.047 107 15 1 2206 2311 31680600 31680706 2.350000e-19 108.0
4 TraesCS1D01G021100 chr1D 83.200 125 14 6 2210 2332 464824324 464824443 2.350000e-19 108.0
5 TraesCS1D01G021100 chr1D 80.000 135 20 7 2201 2332 178417201 178417071 6.590000e-15 93.5
6 TraesCS1D01G021100 chr1D 80.315 127 19 6 2209 2332 434368574 434368451 2.370000e-14 91.6
7 TraesCS1D01G021100 chr1D 80.159 126 19 6 2210 2332 86212504 86212626 8.520000e-14 89.8
8 TraesCS1D01G021100 chr1D 78.832 137 22 7 2199 2332 418571333 418571201 1.100000e-12 86.1
9 TraesCS1D01G021100 chr1D 78.571 126 23 4 2209 2332 460166726 460166849 5.130000e-11 80.5
10 TraesCS1D01G021100 chr1D 77.931 145 19 12 2193 2332 449517864 449518000 1.840000e-10 78.7
11 TraesCS1D01G021100 chr1B 91.739 4249 279 47 1244 5442 13248302 13244076 0.000000e+00 5836.0
12 TraesCS1D01G021100 chr1B 92.586 1214 62 14 1 1199 13249504 13248304 0.000000e+00 1718.0
13 TraesCS1D01G021100 chr1B 87.171 608 68 4 3251 3850 13435243 13435848 0.000000e+00 682.0
14 TraesCS1D01G021100 chr1B 85.030 668 83 10 3184 3850 12944227 12944878 0.000000e+00 664.0
15 TraesCS1D01G021100 chr1B 83.942 685 62 23 3840 4506 12944905 12945559 4.090000e-171 612.0
16 TraesCS1D01G021100 chr1B 82.225 692 77 21 3840 4515 13435875 13436536 6.990000e-154 555.0
17 TraesCS1D01G021100 chr1B 86.166 506 60 8 1709 2211 13434604 13435102 7.040000e-149 538.0
18 TraesCS1D01G021100 chr1B 88.356 292 29 5 3558 3845 12349329 12349619 4.580000e-91 346.0
19 TraesCS1D01G021100 chr1B 89.474 266 27 1 1947 2211 12943654 12943919 9.910000e-88 335.0
20 TraesCS1D01G021100 chr1B 83.204 387 40 12 4789 5171 13436566 13436931 1.280000e-86 331.0
21 TraesCS1D01G021100 chr1B 85.274 292 38 5 3558 3845 13666894 13666604 4.680000e-76 296.0
22 TraesCS1D01G021100 chr1B 84.071 226 24 6 946 1166 12942794 12943012 2.250000e-49 207.0
23 TraesCS1D01G021100 chr1B 83.700 227 23 7 946 1166 13433950 13434168 1.050000e-47 202.0
24 TraesCS1D01G021100 chr1B 84.343 198 26 4 1709 1904 12943454 12943648 8.170000e-44 189.0
25 TraesCS1D01G021100 chr3D 83.031 1267 145 34 3060 4288 15926298 15925064 0.000000e+00 1085.0
26 TraesCS1D01G021100 chr3D 84.424 443 45 12 1771 2209 15926727 15926305 1.240000e-111 414.0
27 TraesCS1D01G021100 chr3D 84.783 230 34 1 4551 4780 340340454 340340226 4.810000e-56 230.0
28 TraesCS1D01G021100 chr3D 77.982 327 51 15 5708 6023 593908602 593908286 1.060000e-42 185.0
29 TraesCS1D01G021100 chr3D 91.667 132 11 0 986 1117 15927854 15927723 3.800000e-42 183.0
30 TraesCS1D01G021100 chr3D 88.000 100 10 2 1785 1883 469374867 469374965 3.910000e-22 117.0
31 TraesCS1D01G021100 chr3D 92.500 80 6 0 3713 3792 15717682 15717603 1.410000e-21 115.0
32 TraesCS1D01G021100 chr3A 81.788 1219 159 32 3060 4219 20713086 20714300 0.000000e+00 963.0
33 TraesCS1D01G021100 chr3A 90.909 484 42 2 5442 5924 740812800 740813282 0.000000e+00 649.0
34 TraesCS1D01G021100 chr3A 90.683 483 43 2 5443 5924 11031349 11031830 5.220000e-180 641.0
35 TraesCS1D01G021100 chr3A 90.062 483 46 2 5443 5924 690939135 690938654 5.250000e-175 625.0
36 TraesCS1D01G021100 chr3A 90.870 471 21 7 5724 6172 740813187 740813657 4.090000e-171 612.0
37 TraesCS1D01G021100 chr3A 90.343 466 41 4 5461 5924 8237504 8237967 5.290000e-170 608.0
38 TraesCS1D01G021100 chr3A 89.787 470 27 7 5724 6172 745479942 745480411 3.210000e-162 582.0
39 TraesCS1D01G021100 chr3A 90.164 427 20 7 5768 6172 743796235 743795809 2.530000e-148 536.0
40 TraesCS1D01G021100 chr3A 82.979 423 50 10 1790 2209 20712676 20713079 4.550000e-96 363.0
41 TraesCS1D01G021100 chr3A 93.233 133 9 0 982 1114 20711223 20711355 4.880000e-46 196.0
42 TraesCS1D01G021100 chr3A 88.571 105 12 0 1789 1893 611945644 611945748 1.810000e-25 128.0
43 TraesCS1D01G021100 chr3A 85.950 121 10 7 5057 5173 20714531 20714648 8.400000e-24 122.0
44 TraesCS1D01G021100 chr3B 84.837 798 101 9 3060 3852 22843406 22842624 0.000000e+00 785.0
45 TraesCS1D01G021100 chr3B 86.449 428 54 4 3862 4288 22842568 22842144 3.370000e-127 466.0
46 TraesCS1D01G021100 chr3B 87.697 317 29 4 1788 2101 22843797 22843488 1.640000e-95 361.0
47 TraesCS1D01G021100 chr3B 91.667 144 12 0 974 1117 22845171 22845028 3.770000e-47 200.0
48 TraesCS1D01G021100 chr3B 88.430 121 11 3 5055 5173 22841664 22841545 6.450000e-30 143.0
49 TraesCS1D01G021100 chr3B 88.889 99 11 0 1785 1883 623655241 623655339 8.400000e-24 122.0
50 TraesCS1D01G021100 chr1A 87.602 613 72 3 3242 3852 10496948 10497558 0.000000e+00 708.0
51 TraesCS1D01G021100 chr1A 82.006 678 67 31 3840 4499 10497583 10498223 5.480000e-145 525.0
52 TraesCS1D01G021100 chr1A 86.826 334 34 7 1879 2211 10496367 10496691 1.260000e-96 364.0
53 TraesCS1D01G021100 chr1A 82.353 221 24 11 951 1166 10495278 10495488 1.770000e-40 178.0
54 TraesCS1D01G021100 chr1A 80.426 235 45 1 4552 4786 32109340 32109573 1.770000e-40 178.0
55 TraesCS1D01G021100 chr1A 82.703 185 29 3 1709 1891 10496133 10496316 1.780000e-35 161.0
56 TraesCS1D01G021100 chr6A 90.702 484 41 4 5443 5924 12048730 12048249 5.220000e-180 641.0
57 TraesCS1D01G021100 chr6A 85.065 462 36 20 5724 6172 12048344 12047903 2.040000e-119 440.0
58 TraesCS1D01G021100 chr6A 78.244 262 52 5 4527 4785 334229012 334229271 4.950000e-36 163.0
59 TraesCS1D01G021100 chr5A 90.456 482 44 2 5443 5923 554052295 554051815 8.730000e-178 634.0
60 TraesCS1D01G021100 chr5A 90.000 470 26 6 5724 6172 3637807 3638276 6.890000e-164 588.0
61 TraesCS1D01G021100 chr5A 80.889 225 41 2 4549 4773 653722080 653722302 6.360000e-40 176.0
62 TraesCS1D01G021100 chr4A 90.021 481 46 2 5445 5924 593659054 593658575 6.800000e-174 621.0
63 TraesCS1D01G021100 chr2A 89.855 483 46 3 5443 5924 751371483 751371003 8.790000e-173 617.0
64 TraesCS1D01G021100 chr2A 88.961 462 35 12 5724 6172 28717972 28718430 1.940000e-154 556.0
65 TraesCS1D01G021100 chr2A 81.481 135 21 4 2209 2341 739692931 739692799 2.350000e-19 108.0
66 TraesCS1D01G021100 chrUn 88.683 486 48 7 5442 5924 63667548 63668029 2.480000e-163 586.0
67 TraesCS1D01G021100 chrUn 88.470 477 32 7 5719 6172 339595 339119 6.990000e-154 555.0
68 TraesCS1D01G021100 chrUn 88.470 477 32 7 5719 6172 314602973 314602497 6.990000e-154 555.0
69 TraesCS1D01G021100 chrUn 88.470 477 32 7 5719 6172 335000711 335001187 6.990000e-154 555.0
70 TraesCS1D01G021100 chrUn 83.333 120 18 2 2214 2332 108450506 108450388 6.540000e-20 110.0
71 TraesCS1D01G021100 chrUn 80.000 125 21 4 2210 2332 470510861 470510983 8.520000e-14 89.8
72 TraesCS1D01G021100 chrUn 78.906 128 21 5 2208 2332 108449855 108449979 1.430000e-11 82.4
73 TraesCS1D01G021100 chrUn 79.339 121 20 3 2192 2308 11056312 11056431 5.130000e-11 80.5
74 TraesCS1D01G021100 chr2D 82.397 267 40 7 4524 4785 56643667 56643403 6.230000e-55 226.0
75 TraesCS1D01G021100 chr2D 81.890 127 17 6 2209 2332 336326799 336326676 1.090000e-17 102.0
76 TraesCS1D01G021100 chr2D 81.890 127 17 6 2209 2332 635084473 635084596 1.090000e-17 102.0
77 TraesCS1D01G021100 chr2D 81.967 122 18 4 2211 2330 615151395 615151514 3.940000e-17 100.0
78 TraesCS1D01G021100 chr7B 83.065 248 36 4 4528 4773 504479918 504480161 2.900000e-53 220.0
79 TraesCS1D01G021100 chr7B 81.154 260 41 5 4528 4785 505937837 505937584 1.050000e-47 202.0
80 TraesCS1D01G021100 chr7D 84.234 222 31 2 4552 4773 478795835 478796052 4.850000e-51 213.0
81 TraesCS1D01G021100 chr7D 81.395 129 24 0 2932 3060 9186291 9186419 8.460000e-19 106.0
82 TraesCS1D01G021100 chr7D 81.343 134 19 6 2202 2332 13509235 13509105 3.040000e-18 104.0
83 TraesCS1D01G021100 chr5D 78.671 286 36 18 5745 6023 559436022 559435755 3.830000e-37 167.0
84 TraesCS1D01G021100 chr5D 83.200 125 17 4 2210 2332 454831779 454831901 1.820000e-20 111.0
85 TraesCS1D01G021100 chr5D 82.540 126 16 6 2210 2332 479784921 479784799 8.460000e-19 106.0
86 TraesCS1D01G021100 chr6D 81.890 127 17 6 2209 2332 344799759 344799882 1.090000e-17 102.0
87 TraesCS1D01G021100 chr4D 80.451 133 22 4 2202 2332 273155776 273155646 1.420000e-16 99.0
88 TraesCS1D01G021100 chr4D 81.395 129 16 7 2208 2332 280416409 280416285 1.420000e-16 99.0
89 TraesCS1D01G021100 chr4D 80.800 125 20 4 2210 2332 416068092 416067970 1.830000e-15 95.3
90 TraesCS1D01G021100 chr4D 80.952 126 18 6 2210 2332 438434014 438434136 1.830000e-15 95.3
91 TraesCS1D01G021100 chr4D 79.851 134 21 6 2202 2332 108317534 108317664 6.590000e-15 93.5
92 TraesCS1D01G021100 chr4D 84.524 84 13 0 4702 4785 129092802 129092885 3.960000e-12 84.2
93 TraesCS1D01G021100 chr4D 81.633 98 16 1 4688 4785 266057861 266057956 5.130000e-11 80.5


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 TraesCS1D01G021100 chr1D 9053727 9059898 6171 False 11398.000000 11398 100.0000 1 6172 1 chr1D.!!$F1 6171
1 TraesCS1D01G021100 chr1B 13244076 13249504 5428 True 3777.000000 5836 92.1625 1 5442 2 chr1B.!!$R2 5441
2 TraesCS1D01G021100 chr1B 13433950 13436931 2981 False 461.600000 682 84.4932 946 5171 5 chr1B.!!$F3 4225
3 TraesCS1D01G021100 chr1B 12942794 12945559 2765 False 401.400000 664 85.3720 946 4506 5 chr1B.!!$F2 3560
4 TraesCS1D01G021100 chr3D 15925064 15927854 2790 True 560.666667 1085 86.3740 986 4288 3 chr3D.!!$R4 3302
5 TraesCS1D01G021100 chr3A 740812800 740813657 857 False 630.500000 649 90.8895 5442 6172 2 chr3A.!!$F6 730
6 TraesCS1D01G021100 chr3A 20711223 20714648 3425 False 411.000000 963 85.9875 982 5173 4 chr3A.!!$F5 4191
7 TraesCS1D01G021100 chr3B 22841545 22845171 3626 True 391.000000 785 87.8160 974 5173 5 chr3B.!!$R1 4199
8 TraesCS1D01G021100 chr1A 10495278 10498223 2945 False 387.200000 708 84.2980 951 4499 5 chr1A.!!$F2 3548
9 TraesCS1D01G021100 chr6A 12047903 12048730 827 True 540.500000 641 87.8835 5443 6172 2 chr6A.!!$R1 729

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
338 339 0.108186 TGGCTGCAAGAGTGTATCCG 60.108 55.000 0.50 0.0 34.07 4.18 F
1205 1228 0.244721 GCAACAAGCTTCACCATCCC 59.755 55.000 0.00 0.0 41.15 3.85 F
1775 2946 0.755686 GGAGTAGTGGGAGGCTGATG 59.244 60.000 0.00 0.0 0.00 3.07 F
2646 3917 0.647410 GATGAGCGACAACACCATCG 59.353 55.000 0.00 0.0 41.32 3.84 F
2653 3924 0.729116 GACAACACCATCGGCATGAG 59.271 55.000 0.00 0.0 30.57 2.90 F
2678 3949 0.815615 GCAAGGGGACGATGTCATCC 60.816 60.000 7.25 0.0 33.68 3.51 F
2731 4002 0.906282 ACGTGGGGACGGGATAGTTT 60.906 55.000 0.00 0.0 37.45 2.66 F
2816 4087 1.069935 GAGGAGGGAGGTAATGCGC 59.930 63.158 0.00 0.0 0.00 6.09 F
2851 4122 1.232909 TCGGGTAGGGGAGAAGAGAT 58.767 55.000 0.00 0.0 0.00 2.75 F
2948 4220 3.056107 CACAGAAACCAGGATTAGGACGA 60.056 47.826 0.00 0.0 0.00 4.20 F
4847 6603 1.489481 AAGTCATCTCGATCAGCCCA 58.511 50.000 0.00 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 2954 0.942962 GCCGATCTGGAGAATGCAAG 59.057 55.000 7.64 0.0 42.00 4.01 R
2442 3684 0.034896 GTCATGTGTTGTCTCGGGGT 59.965 55.000 0.00 0.0 0.00 4.95 R
2673 3944 0.256752 TCGTCTTCCCCTACGGATGA 59.743 55.000 0.00 0.0 41.63 2.92 R
3910 5568 2.561569 ACAGGTGAGGAAAGAACAACG 58.438 47.619 0.00 0.0 0.00 4.10 R
4446 6200 4.646945 TGTGAATTCAGTTTTACCCAAGCA 59.353 37.500 8.80 0.0 0.00 3.91 R
4447 6201 4.982295 GTGTGAATTCAGTTTTACCCAAGC 59.018 41.667 8.80 0.0 0.00 4.01 R
4719 6475 8.287439 TGGAGTCAAGTTTTATGAACTTTCAA 57.713 30.769 6.37 0.0 41.13 2.69 R
4792 6548 2.092429 TGGATCCATACCAAACTGGAGC 60.092 50.000 11.44 0.0 44.45 4.70 R
4827 6583 2.666317 TGGGCTGATCGAGATGACTTA 58.334 47.619 0.00 0.0 0.00 2.24 R
4921 6677 4.200874 TCACCCACTTCGTAAAACATTGT 58.799 39.130 0.00 0.0 0.00 2.71 R
5819 7710 0.975556 TCGGCATAGACCTGCTCCAA 60.976 55.000 0.00 0.0 41.95 3.53 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
86 87 4.985413 AGTTAAAACATGTGGATGCATCG 58.015 39.130 20.15 8.67 32.14 3.84
111 112 6.588719 CCATTTTGTTGGTTAGGAAGATGA 57.411 37.500 0.00 0.00 31.74 2.92
119 120 6.605594 TGTTGGTTAGGAAGATGACTTGTTTT 59.394 34.615 0.00 0.00 36.39 2.43
124 125 7.862873 GGTTAGGAAGATGACTTGTTTTCAAAG 59.137 37.037 0.00 0.00 39.47 2.77
157 158 5.537188 TGTGCAAGTCCCAACAAATTTATC 58.463 37.500 0.00 0.00 0.00 1.75
221 222 7.939784 ATATTACTCAAAGGTCAAGGGAAAC 57.060 36.000 0.00 0.00 0.00 2.78
250 251 5.890334 AGAAACGCCATATACAATGGTTTG 58.110 37.500 5.94 0.05 41.17 2.93
252 253 4.630894 ACGCCATATACAATGGTTTGTG 57.369 40.909 5.94 0.00 45.56 3.33
283 284 4.139038 GTGGGTGCTGTTTAGGTAAAGAA 58.861 43.478 0.00 0.00 0.00 2.52
338 339 0.108186 TGGCTGCAAGAGTGTATCCG 60.108 55.000 0.50 0.00 34.07 4.18
416 417 1.080995 CAAGACTAGAGGCTGTGCGC 61.081 60.000 0.00 0.00 38.13 6.09
417 418 1.536073 AAGACTAGAGGCTGTGCGCA 61.536 55.000 5.66 5.66 41.67 6.09
446 447 6.161381 GTCCAAGTCCTAGTAATCAACGAAA 58.839 40.000 0.00 0.00 0.00 3.46
475 476 1.597663 GGGAATCAAAGTACATCGCGG 59.402 52.381 6.13 0.00 0.00 6.46
476 477 2.546778 GGAATCAAAGTACATCGCGGA 58.453 47.619 6.13 0.00 0.00 5.54
497 498 0.601046 CTCCTCGACAGCACTGCAAA 60.601 55.000 3.30 0.00 0.00 3.68
551 552 5.110814 ACAGCAATGCCCACTATAACTTA 57.889 39.130 0.00 0.00 0.00 2.24
608 609 1.970917 GCCTTGGAAGTGATCACGCG 61.971 60.000 19.85 3.53 36.20 6.01
609 610 1.421485 CTTGGAAGTGATCACGCGC 59.579 57.895 19.85 12.67 36.20 6.86
753 754 5.465390 TCTCAATCCACACTACGAAACAAAG 59.535 40.000 0.00 0.00 0.00 2.77
795 796 8.370266 AGTACTATACATACAAAAGGTCACCA 57.630 34.615 0.00 0.00 0.00 4.17
797 798 6.650120 ACTATACATACAAAAGGTCACCAGG 58.350 40.000 0.00 0.00 0.00 4.45
823 826 2.280183 CGCAAGCTAGATGTCGAAGTTC 59.720 50.000 0.00 0.00 0.00 3.01
866 870 8.225603 AGAAAGACAAGCAAATAAACAGAGAA 57.774 30.769 0.00 0.00 0.00 2.87
891 895 1.745141 GCAGGTGTGGTGATGATCTCC 60.745 57.143 6.59 6.59 0.00 3.71
911 915 0.790207 TTCTCGTCAATGCGTTGAGC 59.210 50.000 21.55 14.58 44.58 4.26
921 925 3.091022 CGTTGAGCGCGCCAAAAC 61.091 61.111 30.33 26.11 0.00 2.43
923 927 4.320928 TTGAGCGCGCCAAAACCG 62.321 61.111 30.33 0.00 0.00 4.44
929 945 4.049640 GCGCCAAAACCGGATGCA 62.050 61.111 9.46 0.00 0.00 3.96
944 960 1.603802 GATGCATATCACAACCACCCG 59.396 52.381 0.00 0.00 33.38 5.28
961 977 1.447489 CGCTCTCCTGCTTCCACAG 60.447 63.158 0.00 0.00 37.42 3.66
1023 1045 1.674221 GCGAGACACTTCCTGCTCAAT 60.674 52.381 0.00 0.00 0.00 2.57
1117 1139 4.680237 CCGCCGTCAAGGTCTGCA 62.680 66.667 0.00 0.00 43.70 4.41
1118 1140 3.114616 CGCCGTCAAGGTCTGCAG 61.115 66.667 7.63 7.63 43.70 4.41
1119 1141 2.031163 GCCGTCAAGGTCTGCAGT 59.969 61.111 14.67 0.00 43.70 4.40
1120 1142 2.029844 GCCGTCAAGGTCTGCAGTC 61.030 63.158 14.67 8.19 43.70 3.51
1205 1228 0.244721 GCAACAAGCTTCACCATCCC 59.755 55.000 0.00 0.00 41.15 3.85
1249 1283 0.902531 ATCCACCCCTTCGTACTGTG 59.097 55.000 0.00 0.00 0.00 3.66
1292 1330 3.561503 CGACAAGATCGCCAATCGTATA 58.438 45.455 0.00 0.00 45.52 1.47
1294 1332 5.329493 CGACAAGATCGCCAATCGTATATA 58.671 41.667 0.00 0.00 45.52 0.86
1455 1719 6.819397 AAATAGCTTTTGGTTAGTCCTGTC 57.181 37.500 0.00 0.00 37.07 3.51
1477 1742 9.950680 CTGTCTGTTCTTTTTAATGTGTGTATT 57.049 29.630 0.00 0.00 0.00 1.89
1527 1842 5.300286 AGAAAAGCAAGACAGCAACATAACT 59.700 36.000 0.00 0.00 36.85 2.24
1632 1960 6.659824 TCAGATAAAGGGTTAATTCAGGACC 58.340 40.000 0.00 0.00 0.00 4.46
1642 1970 6.649141 GGGTTAATTCAGGACCATTTTGAAAC 59.351 38.462 0.00 0.00 34.80 2.78
1645 1973 8.711457 GTTAATTCAGGACCATTTTGAAACATG 58.289 33.333 0.00 0.00 34.80 3.21
1670 1999 0.949397 CCAGATTGACATGGCATCCG 59.051 55.000 0.00 0.00 0.00 4.18
1775 2946 0.755686 GGAGTAGTGGGAGGCTGATG 59.244 60.000 0.00 0.00 0.00 3.07
1781 2952 1.211457 AGTGGGAGGCTGATGTCAATC 59.789 52.381 0.00 0.00 0.00 2.67
1783 2954 1.065199 TGGGAGGCTGATGTCAATCAC 60.065 52.381 0.00 0.00 37.91 3.06
1791 2962 4.103357 GCTGATGTCAATCACTTGCATTC 58.897 43.478 0.00 0.00 37.91 2.67
1802 2973 0.942962 CTTGCATTCTCCAGATCGGC 59.057 55.000 0.00 0.00 33.14 5.54
1838 3009 7.735326 AAAGCTATTTGAAGAGGAGGTAGTA 57.265 36.000 0.00 0.00 0.00 1.82
1893 3126 2.714250 TGGTAACCCAAATCTCTGGTGT 59.286 45.455 0.00 0.00 37.98 4.16
2142 3376 4.276431 CAGTACCCGAGTTCCTCTATTCTC 59.724 50.000 0.00 0.00 0.00 2.87
2143 3377 3.673543 ACCCGAGTTCCTCTATTCTCT 57.326 47.619 0.00 0.00 0.00 3.10
2235 3469 6.800072 AAAAAGTATGTTTTTGGTCCCTCA 57.200 33.333 0.83 0.00 0.00 3.86
2243 3477 2.358322 TTTGGTCCCTCAAGTTCACC 57.642 50.000 0.00 0.00 0.00 4.02
2265 3499 6.262193 CCAAAAGTATACATTTGGTCCGTT 57.738 37.500 31.09 3.30 44.91 4.44
2270 3504 5.562635 AGTATACATTTGGTCCGTTGGAAA 58.437 37.500 5.50 0.00 31.38 3.13
2274 3508 5.793030 ACATTTGGTCCGTTGGAAATTTA 57.207 34.783 0.00 0.00 31.38 1.40
2286 3520 9.238368 TCCGTTGGAAATTTATAGAAGACATTT 57.762 29.630 0.00 0.00 0.00 2.32
2313 3547 5.763204 TCCTACAAATCTCAAAACCAGACAC 59.237 40.000 0.00 0.00 0.00 3.67
2318 3552 7.330262 ACAAATCTCAAAACCAGACACAATTT 58.670 30.769 0.00 0.00 0.00 1.82
2319 3553 8.474025 ACAAATCTCAAAACCAGACACAATTTA 58.526 29.630 0.00 0.00 0.00 1.40
2328 3562 6.096673 ACCAGACACAATTTATCCAAAACC 57.903 37.500 0.00 0.00 0.00 3.27
2334 3568 8.650490 AGACACAATTTATCCAAAACCAGAAAT 58.350 29.630 0.00 0.00 0.00 2.17
2340 3574 6.662865 TTATCCAAAACCAGAAATGAAGCA 57.337 33.333 0.00 0.00 0.00 3.91
2341 3575 4.589216 TCCAAAACCAGAAATGAAGCAG 57.411 40.909 0.00 0.00 0.00 4.24
2344 3578 5.596361 TCCAAAACCAGAAATGAAGCAGTAA 59.404 36.000 0.00 0.00 0.00 2.24
2349 3583 9.515226 AAAACCAGAAATGAAGCAGTAATAGTA 57.485 29.630 0.00 0.00 0.00 1.82
2360 3594 8.531982 TGAAGCAGTAATAGTATGATATGTCCC 58.468 37.037 0.00 0.00 0.00 4.46
2361 3595 7.425224 AGCAGTAATAGTATGATATGTCCCC 57.575 40.000 0.00 0.00 0.00 4.81
2381 3615 3.550030 CCCGGTTTTGACTGAAACATCAC 60.550 47.826 0.00 0.00 40.44 3.06
2403 3637 1.968540 GACTGCCACCTGCTGGTTC 60.969 63.158 13.36 8.55 46.05 3.62
2429 3663 4.052229 CTCGGCTCCCACGTCGTT 62.052 66.667 0.00 0.00 0.00 3.85
2430 3664 4.351938 TCGGCTCCCACGTCGTTG 62.352 66.667 0.00 0.00 0.00 4.10
2432 3666 2.029964 GGCTCCCACGTCGTTGAA 59.970 61.111 0.00 0.00 0.00 2.69
2435 3669 1.300620 CTCCCACGTCGTTGAAGCA 60.301 57.895 0.00 0.00 0.00 3.91
2442 3684 0.933047 CGTCGTTGAAGCACTCGTGA 60.933 55.000 0.39 0.00 0.00 4.35
2465 3707 2.061773 CCGAGACAACACATGACTCAC 58.938 52.381 0.00 0.00 46.84 3.51
2469 3711 1.867233 GACAACACATGACTCACGCTT 59.133 47.619 0.00 0.00 0.00 4.68
2470 3712 1.867233 ACAACACATGACTCACGCTTC 59.133 47.619 0.00 0.00 0.00 3.86
2472 3715 0.667487 ACACATGACTCACGCTTCCG 60.667 55.000 0.00 0.00 41.14 4.30
2477 3720 0.671796 TGACTCACGCTTCCGAGAAA 59.328 50.000 0.00 0.00 33.81 2.52
2500 3743 2.180769 CGAACTCGATCGGCACCA 59.819 61.111 16.41 0.00 43.02 4.17
2509 3752 2.852495 GATCGGCACCACATCACCGT 62.852 60.000 0.00 0.00 45.76 4.83
2518 3761 1.003839 ACATCACCGTCATTGCCGT 60.004 52.632 0.00 0.00 0.00 5.68
2520 3763 2.398554 ATCACCGTCATTGCCGTGC 61.399 57.895 0.00 0.00 0.00 5.34
2545 3816 2.189499 GCCGGCACTTCATGGATCC 61.189 63.158 24.80 4.20 0.00 3.36
2563 3834 1.566018 CCGGTGTGGAAGCTTCGAAC 61.566 60.000 19.91 19.40 42.00 3.95
2591 3862 4.749310 CGCCGAGCACTTGAGCCT 62.749 66.667 0.00 0.00 34.23 4.58
2599 3870 1.447489 CACTTGAGCCTGAGAGCGG 60.447 63.158 0.00 0.00 38.01 5.52
2600 3871 1.910772 ACTTGAGCCTGAGAGCGGT 60.911 57.895 0.00 0.00 38.01 5.68
2609 3880 2.512515 GAGAGCGGTGTGGCCATC 60.513 66.667 9.72 5.40 36.97 3.51
2617 3888 1.599518 GTGTGGCCATCGTTGACCA 60.600 57.895 9.72 0.00 0.00 4.02
2630 3901 2.516923 GTTGACCACGTCGACTAGATG 58.483 52.381 14.70 6.51 42.05 2.90
2631 3902 2.103537 TGACCACGTCGACTAGATGA 57.896 50.000 14.70 0.00 39.17 2.92
2632 3903 2.007608 TGACCACGTCGACTAGATGAG 58.992 52.381 14.70 0.00 39.17 2.90
2633 3904 0.733729 ACCACGTCGACTAGATGAGC 59.266 55.000 14.70 0.00 39.17 4.26
2636 3907 0.651551 ACGTCGACTAGATGAGCGAC 59.348 55.000 14.70 0.00 44.36 5.19
2637 3908 0.651031 CGTCGACTAGATGAGCGACA 59.349 55.000 14.70 0.00 46.26 4.35
2638 3909 1.062148 CGTCGACTAGATGAGCGACAA 59.938 52.381 14.70 0.00 46.26 3.18
2641 3912 2.159558 TCGACTAGATGAGCGACAACAC 60.160 50.000 0.00 0.00 31.58 3.32
2642 3913 2.531206 GACTAGATGAGCGACAACACC 58.469 52.381 0.00 0.00 0.00 4.16
2643 3914 1.893137 ACTAGATGAGCGACAACACCA 59.107 47.619 0.00 0.00 0.00 4.17
2644 3915 2.497675 ACTAGATGAGCGACAACACCAT 59.502 45.455 0.00 0.00 0.00 3.55
2645 3916 2.015736 AGATGAGCGACAACACCATC 57.984 50.000 0.00 0.00 35.21 3.51
2646 3917 0.647410 GATGAGCGACAACACCATCG 59.353 55.000 0.00 0.00 41.32 3.84
2647 3918 0.740868 ATGAGCGACAACACCATCGG 60.741 55.000 0.00 0.00 38.78 4.18
2648 3919 2.740714 GAGCGACAACACCATCGGC 61.741 63.158 0.00 0.00 38.78 5.54
2649 3920 3.047280 GCGACAACACCATCGGCA 61.047 61.111 0.00 0.00 38.78 5.69
2650 3921 2.398554 GCGACAACACCATCGGCAT 61.399 57.895 0.00 0.00 38.78 4.40
2651 3922 1.425031 CGACAACACCATCGGCATG 59.575 57.895 0.00 0.00 34.67 4.06
2652 3923 1.018752 CGACAACACCATCGGCATGA 61.019 55.000 0.00 0.00 34.67 3.07
2653 3924 0.729116 GACAACACCATCGGCATGAG 59.271 55.000 0.00 0.00 30.57 2.90
2661 3932 2.970379 ATCGGCATGAGGTGGTGCA 61.970 57.895 0.00 0.00 43.00 4.57
2668 3939 2.034221 GAGGTGGTGCAAGGGGAC 59.966 66.667 0.00 0.00 34.10 4.46
2673 3944 2.351276 GGTGCAAGGGGACGATGT 59.649 61.111 0.00 0.00 36.00 3.06
2675 3946 1.003839 GTGCAAGGGGACGATGTCA 60.004 57.895 0.00 0.00 33.68 3.58
2678 3949 0.815615 GCAAGGGGACGATGTCATCC 60.816 60.000 7.25 0.00 33.68 3.51
2710 3981 2.641559 GCACCAAGCAGCAGTGAC 59.358 61.111 12.93 2.86 44.79 3.67
2712 3983 1.595109 CACCAAGCAGCAGTGACGA 60.595 57.895 0.00 0.00 33.21 4.20
2714 3985 2.661566 CCAAGCAGCAGTGACGACG 61.662 63.158 0.00 0.00 0.00 5.12
2723 3994 4.712425 GTGACGACGTGGGGACGG 62.712 72.222 4.58 0.00 37.45 4.79
2727 3998 2.829914 CGACGTGGGGACGGGATA 60.830 66.667 0.00 0.00 37.45 2.59
2731 4002 0.906282 ACGTGGGGACGGGATAGTTT 60.906 55.000 0.00 0.00 37.45 2.66
2736 4007 1.087771 GGGACGGGATAGTTTGTGCG 61.088 60.000 0.00 0.00 0.00 5.34
2738 4009 1.702491 GACGGGATAGTTTGTGCGGC 61.702 60.000 0.00 0.00 0.00 6.53
2765 4036 2.343758 CGGTGTGACTGACTGGGG 59.656 66.667 0.00 0.00 0.00 4.96
2766 4037 2.750350 GGTGTGACTGACTGGGGG 59.250 66.667 0.00 0.00 0.00 5.40
2768 4039 1.674057 GTGTGACTGACTGGGGGAG 59.326 63.158 0.00 0.00 0.00 4.30
2810 4081 4.643930 TCCAGGAGGAGGGAGGTA 57.356 61.111 0.00 0.00 39.61 3.08
2812 4083 1.330155 TCCAGGAGGAGGGAGGTAAT 58.670 55.000 0.00 0.00 39.61 1.89
2816 4087 1.069935 GAGGAGGGAGGTAATGCGC 59.930 63.158 0.00 0.00 0.00 6.09
2834 4105 1.577328 GCTGGTGGTGGATGTGTTCG 61.577 60.000 0.00 0.00 0.00 3.95
2851 4122 1.232909 TCGGGTAGGGGAGAAGAGAT 58.767 55.000 0.00 0.00 0.00 2.75
2881 4153 3.448469 AAAAAGGCCCATCCAACGA 57.552 47.368 0.00 0.00 37.29 3.85
2948 4220 3.056107 CACAGAAACCAGGATTAGGACGA 60.056 47.826 0.00 0.00 0.00 4.20
2952 4224 5.648092 CAGAAACCAGGATTAGGACGAAATT 59.352 40.000 0.00 0.00 0.00 1.82
2953 4225 6.151144 CAGAAACCAGGATTAGGACGAAATTT 59.849 38.462 0.00 0.00 0.00 1.82
2955 4227 8.053355 AGAAACCAGGATTAGGACGAAATTTAT 58.947 33.333 0.00 0.00 0.00 1.40
2958 4230 6.992715 ACCAGGATTAGGACGAAATTTATCTG 59.007 38.462 0.00 0.00 0.00 2.90
2963 4235 8.406297 GGATTAGGACGAAATTTATCTGCTTTT 58.594 33.333 0.00 0.00 0.00 2.27
2986 4258 7.979444 TTGAAACTTGAAGGACGAAATATCT 57.021 32.000 0.00 0.00 0.00 1.98
3048 4321 9.281371 GTGAACTTAAGGGACTAAAAACATACT 57.719 33.333 7.53 0.00 38.49 2.12
3100 4373 4.277476 TCACCAGGAATTGAACACTTGTT 58.723 39.130 0.00 0.00 41.64 2.83
3185 4462 6.806751 AGTCTATCGTGTGTTATTGCTATGT 58.193 36.000 0.00 0.00 0.00 2.29
3255 4803 5.593909 CACATGTGCCCTATTCCTTGAATTA 59.406 40.000 13.94 0.00 33.95 1.40
3346 4895 5.181245 AGTGTTAATGATTTCCGGTGTCAAG 59.819 40.000 0.00 0.00 0.00 3.02
3358 4907 4.273969 TCCGGTGTCAAGTTGTTAATTGTC 59.726 41.667 0.00 0.00 0.00 3.18
3453 5047 8.335356 TGAGTTTTATCTCTTTTGTTGTTCGAG 58.665 33.333 0.00 0.00 35.68 4.04
3473 5073 4.496673 CGAGAGATTCTTCTGGTACCTTCG 60.497 50.000 14.36 1.70 30.30 3.79
3485 5085 3.198200 TGGTACCTTCGGCTTAGCATTAA 59.802 43.478 14.36 0.00 0.00 1.40
3852 5456 9.569167 CGTTCATCTTAGTGTAAGTCTGATTAA 57.431 33.333 0.00 0.00 37.10 1.40
4389 6134 5.124457 GCTTGAAACACCAGTGTATCATGAT 59.876 40.000 13.81 13.81 44.13 2.45
4446 6200 9.515226 TCACTCTTAAAATGGCAGTATTAGTTT 57.485 29.630 0.00 0.00 0.00 2.66
4447 6201 9.559958 CACTCTTAAAATGGCAGTATTAGTTTG 57.440 33.333 0.00 0.00 0.00 2.93
4567 6323 9.502091 TGTTCACTCACATATTAGCTTTTACTT 57.498 29.630 0.00 0.00 0.00 2.24
4743 6499 8.188139 TGTTGAAAGTTCATAAAACTTGACTCC 58.812 33.333 4.09 0.00 40.10 3.85
4787 6543 8.478877 AGAGTAAATAAACATAGAGGGAGTGTG 58.521 37.037 0.00 0.00 0.00 3.82
4792 6548 9.838339 AAATAAACATAGAGGGAGTGTGAATAG 57.162 33.333 0.00 0.00 0.00 1.73
4827 6583 6.069963 GGTATGGATCCACCTAAGATAAGCAT 60.070 42.308 18.99 0.00 39.86 3.79
4847 6603 1.489481 AAGTCATCTCGATCAGCCCA 58.511 50.000 0.00 0.00 0.00 5.36
4921 6677 5.066593 TCATAATACCGTGGCATGCAATTA 58.933 37.500 21.36 12.35 0.00 1.40
5043 6822 6.954487 TTCCCTTTTAAGACCTTTTCACTC 57.046 37.500 0.00 0.00 0.00 3.51
5173 6957 2.026636 TCTGGGACGGTGAAATTTAGGG 60.027 50.000 0.00 0.00 35.30 3.53
5174 6958 1.004979 TGGGACGGTGAAATTTAGGGG 59.995 52.381 0.00 0.00 0.00 4.79
5182 6966 4.610333 GGTGAAATTTAGGGGTCATCCTT 58.390 43.478 0.00 0.00 38.30 3.36
5185 6969 5.952347 GTGAAATTTAGGGGTCATCCTTCTT 59.048 40.000 0.00 0.00 38.30 2.52
5186 6970 6.437477 GTGAAATTTAGGGGTCATCCTTCTTT 59.563 38.462 0.00 0.00 38.30 2.52
5187 6971 7.016296 TGAAATTTAGGGGTCATCCTTCTTTT 58.984 34.615 0.00 0.00 38.30 2.27
5189 6973 2.789409 AGGGGTCATCCTTCTTTTCG 57.211 50.000 0.00 0.00 32.13 3.46
5249 7034 6.071728 GCCATGGCTGCTAAATTCAGTTATAT 60.072 38.462 29.98 0.00 38.26 0.86
5250 7035 7.533426 CCATGGCTGCTAAATTCAGTTATATC 58.467 38.462 0.00 0.00 34.21 1.63
5253 7038 6.646653 TGGCTGCTAAATTCAGTTATATCGAG 59.353 38.462 0.00 0.00 34.21 4.04
5258 7043 5.907197 AAATTCAGTTATATCGAGTGCGG 57.093 39.130 0.00 0.00 38.28 5.69
5264 7049 4.207224 CAGTTATATCGAGTGCGGAAACAG 59.793 45.833 0.00 0.00 38.28 3.16
5272 7057 1.625818 AGTGCGGAAACAGGAATCTCT 59.374 47.619 0.00 0.00 0.00 3.10
5273 7058 1.734465 GTGCGGAAACAGGAATCTCTG 59.266 52.381 0.00 0.00 40.40 3.35
5278 7063 3.433615 CGGAAACAGGAATCTCTGTGAAC 59.566 47.826 5.40 1.96 46.17 3.18
5313 7098 5.407502 TGTAACTGTGATTATCACCGTCTG 58.592 41.667 19.62 9.36 46.40 3.51
5325 7110 1.080230 CCGTCTGGTGAGCAGTCAG 60.080 63.158 11.78 4.43 31.53 3.51
5330 7115 2.233431 GTCTGGTGAGCAGTCAGAAGAT 59.767 50.000 11.78 0.00 38.97 2.40
5331 7116 2.233186 TCTGGTGAGCAGTCAGAAGATG 59.767 50.000 11.78 0.00 34.97 2.90
5342 7127 6.496218 AGCAGTCAGAAGATGGATCATGTATA 59.504 38.462 0.00 0.00 0.00 1.47
5344 7129 7.525194 GCAGTCAGAAGATGGATCATGTATACT 60.525 40.741 4.17 0.00 0.00 2.12
5346 7131 9.019656 AGTCAGAAGATGGATCATGTATACTAC 57.980 37.037 4.17 0.00 0.00 2.73
5355 7140 7.399634 TGGATCATGTATACTACGGAGATACA 58.600 38.462 17.01 17.01 39.65 2.29
5435 7221 6.385766 GATCTCAGGGATCCCTAAAATGAT 57.614 41.667 33.41 26.45 46.28 2.45
5494 7280 2.507854 GGCCGTCAGCATAGCCCTA 61.508 63.158 0.00 0.00 46.50 3.53
5496 7282 0.880718 GCCGTCAGCATAGCCCTAAC 60.881 60.000 0.00 0.00 42.97 2.34
5621 7407 1.551452 GCATAGGCCCTATCTCGACT 58.449 55.000 0.00 0.00 0.00 4.18
5705 7491 1.891919 TCAAGTGCTGACCAACGCC 60.892 57.895 0.00 0.00 0.00 5.68
5706 7492 2.594592 AAGTGCTGACCAACGCCC 60.595 61.111 0.00 0.00 0.00 6.13
5814 7705 2.993264 ACATGGCAGCAACTGGGC 60.993 61.111 0.00 0.00 31.21 5.36
5815 7706 2.992689 CATGGCAGCAACTGGGCA 60.993 61.111 0.00 0.00 44.07 5.36
5819 7710 2.282040 GCAGCAACTGGGCACTCT 60.282 61.111 0.00 0.00 35.83 3.24
5829 7720 2.753029 GGCACTCTTGGAGCAGGT 59.247 61.111 0.00 0.00 32.04 4.00
5907 7798 1.079127 GCATAGACCTGCCACGTGT 60.079 57.895 15.65 0.00 36.10 4.49
6045 7958 0.403655 TCACATAACAGCTGGCCCAA 59.596 50.000 19.93 0.00 0.00 4.12
6102 8015 3.687572 AGAAGCATCGCAAAGCATAAG 57.312 42.857 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.538047 ACTTGCACACATGATGACCC 58.462 50.000 0.00 0.00 0.00 4.46
48 49 4.764679 TTAACTTGCACACATGATGACC 57.235 40.909 0.00 0.00 0.00 4.02
111 112 5.010012 CAGATAGCCCACTTTGAAAACAAGT 59.990 40.000 0.00 0.00 34.67 3.16
119 120 1.350684 TGCACAGATAGCCCACTTTGA 59.649 47.619 0.00 0.00 0.00 2.69
124 125 1.373570 GACTTGCACAGATAGCCCAC 58.626 55.000 0.00 0.00 0.00 4.61
157 158 5.659440 ACACACAAGCCCCAATATTTAAG 57.341 39.130 0.00 0.00 0.00 1.85
212 213 3.115554 CGTTTCTTGCTTGTTTCCCTTG 58.884 45.455 0.00 0.00 0.00 3.61
221 222 4.614555 TGTATATGGCGTTTCTTGCTTG 57.385 40.909 0.00 0.00 0.00 4.01
250 251 0.104671 AGCACCCACAATTTGCACAC 59.895 50.000 2.16 0.00 38.81 3.82
252 253 0.104671 ACAGCACCCACAATTTGCAC 59.895 50.000 2.16 0.00 38.81 4.57
283 284 7.367186 CCCCTTTTATCCATATCATCCATAGCT 60.367 40.741 0.00 0.00 0.00 3.32
416 417 0.903454 ACTAGGACTTGGACCCCGTG 60.903 60.000 0.00 0.00 0.00 4.94
417 418 0.706433 TACTAGGACTTGGACCCCGT 59.294 55.000 0.00 0.00 0.00 5.28
446 447 5.876357 TGTACTTTGATTCCCTGCTAAACT 58.124 37.500 0.00 0.00 0.00 2.66
460 461 0.530744 AGCTCCGCGATGTACTTTGA 59.469 50.000 8.23 0.00 0.00 2.69
475 476 1.153862 CAGTGCTGTCGAGGAGCTC 60.154 63.158 15.51 4.71 37.35 4.09
476 477 2.969016 CAGTGCTGTCGAGGAGCT 59.031 61.111 15.51 0.00 37.35 4.09
497 498 4.993705 TGTTCCCATCTACTCCAAGTTT 57.006 40.909 0.00 0.00 0.00 2.66
551 552 3.119637 CCAATTTCGCGTCCCACTAAAAT 60.120 43.478 5.77 0.00 0.00 1.82
561 562 1.797537 GTGCAGCCAATTTCGCGTC 60.798 57.895 5.77 0.00 0.00 5.19
608 609 5.526846 CACCAATTCCTCTCTTCTTATCTGC 59.473 44.000 0.00 0.00 0.00 4.26
609 610 6.882656 TCACCAATTCCTCTCTTCTTATCTG 58.117 40.000 0.00 0.00 0.00 2.90
706 707 8.335532 AGATTCGGTGTTGATCTGATTTTAAA 57.664 30.769 0.00 0.00 0.00 1.52
770 771 8.370266 TGGTGACCTTTTGTATGTATAGTACT 57.630 34.615 2.11 0.00 0.00 2.73
795 796 1.276421 ACATCTAGCTTGCGTTGTCCT 59.724 47.619 0.00 0.00 0.00 3.85
797 798 1.321743 CGACATCTAGCTTGCGTTGTC 59.678 52.381 0.00 3.72 0.00 3.18
802 803 1.914634 ACTTCGACATCTAGCTTGCG 58.085 50.000 0.00 0.00 0.00 4.85
860 864 0.679002 CACACCTGCCCCATTCTCTG 60.679 60.000 0.00 0.00 0.00 3.35
866 870 2.240918 ATCACCACACCTGCCCCAT 61.241 57.895 0.00 0.00 0.00 4.00
891 895 1.201855 GCTCAACGCATTGACGAGAAG 60.202 52.381 0.00 0.00 40.01 2.85
913 917 0.667993 ATATGCATCCGGTTTTGGCG 59.332 50.000 0.19 0.00 0.00 5.69
914 918 1.680735 TGATATGCATCCGGTTTTGGC 59.319 47.619 0.19 0.00 0.00 4.52
921 925 1.603802 GTGGTTGTGATATGCATCCGG 59.396 52.381 0.19 0.00 0.00 5.14
923 927 1.956477 GGGTGGTTGTGATATGCATCC 59.044 52.381 0.19 0.00 0.00 3.51
929 945 1.139058 GAGAGCGGGTGGTTGTGATAT 59.861 52.381 0.00 0.00 0.00 1.63
944 960 0.390998 GACTGTGGAAGCAGGAGAGC 60.391 60.000 0.00 0.00 40.59 4.09
961 977 2.099405 CTCTCTCTCTCAACAGGGGAC 58.901 57.143 0.00 0.00 0.00 4.46
1008 1030 1.066143 CCCGTATTGAGCAGGAAGTGT 60.066 52.381 0.00 0.00 0.00 3.55
1023 1045 2.792947 GGGCATCTTCGCTCCCGTA 61.793 63.158 0.00 0.00 35.54 4.02
1115 1137 0.539051 AGGAGGTATGTGCAGACTGC 59.461 55.000 20.86 20.86 45.29 4.40
1116 1138 1.137872 GGAGGAGGTATGTGCAGACTG 59.862 57.143 0.00 0.00 0.00 3.51
1117 1139 1.007721 AGGAGGAGGTATGTGCAGACT 59.992 52.381 0.00 0.00 0.00 3.24
1118 1140 1.490574 AGGAGGAGGTATGTGCAGAC 58.509 55.000 0.00 0.00 0.00 3.51
1119 1141 3.619900 ATAGGAGGAGGTATGTGCAGA 57.380 47.619 0.00 0.00 0.00 4.26
1120 1142 4.696479 AAATAGGAGGAGGTATGTGCAG 57.304 45.455 0.00 0.00 0.00 4.41
1146 1168 2.029844 GGTGAAGCGAGTGGTGAGC 61.030 63.158 0.00 0.00 0.00 4.26
1157 1180 4.525912 AAAAGATGGTGATTGGTGAAGC 57.474 40.909 0.00 0.00 0.00 3.86
1185 1208 0.961019 GGATGGTGAAGCTTGTTGCA 59.039 50.000 2.10 0.00 45.94 4.08
1221 1255 2.854523 GGGGTGGATAGAGGGGGC 60.855 72.222 0.00 0.00 0.00 5.80
1249 1283 7.698970 TGTCGAAGATAAAAACAAGGAAACAAC 59.301 33.333 0.00 0.00 40.67 3.32
1287 1325 9.817365 CCAGAAGCAATTGAGAAATTATATACG 57.183 33.333 10.34 0.00 0.00 3.06
1292 1330 6.183360 CGACCCAGAAGCAATTGAGAAATTAT 60.183 38.462 10.34 0.00 0.00 1.28
1294 1332 4.082571 CGACCCAGAAGCAATTGAGAAATT 60.083 41.667 10.34 0.00 0.00 1.82
1446 1710 7.990886 ACACATTAAAAAGAACAGACAGGACTA 59.009 33.333 0.00 0.00 0.00 2.59
1477 1742 2.627945 CGTTTGCAAGGGTAGCAGATA 58.372 47.619 0.00 0.00 43.75 1.98
1527 1842 4.792068 ACAGAAGAAATTCCCAGTGTGAA 58.208 39.130 0.00 0.00 0.00 3.18
1632 1960 3.991773 CTGGCCACTCATGTTTCAAAATG 59.008 43.478 0.00 0.00 0.00 2.32
1642 1970 2.118313 TGTCAATCTGGCCACTCATG 57.882 50.000 0.00 0.00 0.00 3.07
1645 1973 1.386533 CCATGTCAATCTGGCCACTC 58.613 55.000 0.00 0.00 0.00 3.51
1775 2946 4.005650 TCTGGAGAATGCAAGTGATTGAC 58.994 43.478 0.00 0.00 34.45 3.18
1781 2952 1.938577 CCGATCTGGAGAATGCAAGTG 59.061 52.381 0.00 0.00 42.00 3.16
1783 2954 0.942962 GCCGATCTGGAGAATGCAAG 59.057 55.000 7.64 0.00 42.00 4.01
1791 2962 2.587194 CGCCAAGCCGATCTGGAG 60.587 66.667 2.97 0.00 42.00 3.86
1831 3002 4.463186 ACAGATCTTCACGCTTTACTACCT 59.537 41.667 0.00 0.00 0.00 3.08
1838 3009 5.122396 GGTGATAAACAGATCTTCACGCTTT 59.878 40.000 15.09 2.70 38.02 3.51
1893 3126 9.491675 CCTCGATAGACAGAACTACTAAGATAA 57.508 37.037 0.00 0.00 42.67 1.75
1959 3192 7.878127 TCCAAAGAAGTTAGATGAGAACGATTT 59.122 33.333 0.00 0.00 31.85 2.17
2212 3446 6.800072 TGAGGGACCAAAAACATACTTTTT 57.200 33.333 0.00 0.00 32.38 1.94
2218 3452 5.300792 GTGAACTTGAGGGACCAAAAACATA 59.699 40.000 0.00 0.00 0.00 2.29
2243 3477 6.072397 TCCAACGGACCAAATGTATACTTTTG 60.072 38.462 26.11 26.11 39.36 2.44
2261 3495 9.289303 CAAATGTCTTCTATAAATTTCCAACGG 57.711 33.333 0.00 0.00 0.00 4.44
2265 3499 8.966868 GGACCAAATGTCTTCTATAAATTTCCA 58.033 33.333 0.00 0.00 43.89 3.53
2274 3508 8.552296 AGATTTGTAGGACCAAATGTCTTCTAT 58.448 33.333 4.04 0.00 43.28 1.98
2286 3520 5.055265 TGGTTTTGAGATTTGTAGGACCA 57.945 39.130 0.00 0.00 32.66 4.02
2291 3525 6.618287 TGTGTCTGGTTTTGAGATTTGTAG 57.382 37.500 0.00 0.00 0.00 2.74
2293 3527 5.913137 TTGTGTCTGGTTTTGAGATTTGT 57.087 34.783 0.00 0.00 0.00 2.83
2297 3531 7.451255 TGGATAAATTGTGTCTGGTTTTGAGAT 59.549 33.333 0.00 0.00 0.00 2.75
2313 3547 8.445493 GCTTCATTTCTGGTTTTGGATAAATTG 58.555 33.333 0.00 0.00 0.00 2.32
2318 3552 5.774690 ACTGCTTCATTTCTGGTTTTGGATA 59.225 36.000 0.00 0.00 0.00 2.59
2319 3553 4.590222 ACTGCTTCATTTCTGGTTTTGGAT 59.410 37.500 0.00 0.00 0.00 3.41
2334 3568 8.531982 GGGACATATCATACTATTACTGCTTCA 58.468 37.037 0.00 0.00 0.00 3.02
2340 3574 6.500336 ACCGGGGACATATCATACTATTACT 58.500 40.000 6.32 0.00 0.00 2.24
2341 3575 6.786967 ACCGGGGACATATCATACTATTAC 57.213 41.667 6.32 0.00 0.00 1.89
2344 3578 6.271391 TCAAAACCGGGGACATATCATACTAT 59.729 38.462 6.32 0.00 0.00 2.12
2349 3583 3.202151 AGTCAAAACCGGGGACATATCAT 59.798 43.478 6.32 0.00 34.04 2.45
2359 3593 2.621055 TGATGTTTCAGTCAAAACCGGG 59.379 45.455 6.32 0.00 38.16 5.73
2360 3594 3.628017 GTGATGTTTCAGTCAAAACCGG 58.372 45.455 0.00 0.00 38.16 5.28
2361 3595 3.242608 ACGTGATGTTTCAGTCAAAACCG 60.243 43.478 0.00 0.00 38.16 4.44
2423 3657 0.933047 TCACGAGTGCTTCAACGACG 60.933 55.000 0.00 0.00 0.00 5.12
2429 3663 2.741092 GGGGTCACGAGTGCTTCA 59.259 61.111 0.00 0.00 0.00 3.02
2430 3664 2.432628 CGGGGTCACGAGTGCTTC 60.433 66.667 0.00 0.00 35.47 3.86
2442 3684 0.034896 GTCATGTGTTGTCTCGGGGT 59.965 55.000 0.00 0.00 0.00 4.95
2485 3728 0.460284 GATGTGGTGCCGATCGAGTT 60.460 55.000 18.66 0.00 0.00 3.01
2490 3733 2.173669 CGGTGATGTGGTGCCGATC 61.174 63.158 0.00 0.00 46.33 3.69
2491 3734 2.125147 CGGTGATGTGGTGCCGAT 60.125 61.111 0.00 0.00 46.33 4.18
2495 3738 0.168788 CAATGACGGTGATGTGGTGC 59.831 55.000 0.00 0.00 0.00 5.01
2500 3743 1.003839 ACGGCAATGACGGTGATGT 60.004 52.632 14.88 0.00 39.02 3.06
2528 3771 1.889105 CGGATCCATGAAGTGCCGG 60.889 63.158 13.41 0.00 35.42 6.13
2529 3772 1.889105 CCGGATCCATGAAGTGCCG 60.889 63.158 13.41 0.00 38.54 5.69
2536 3779 0.541392 CTTCCACACCGGATCCATGA 59.459 55.000 17.83 0.00 45.80 3.07
2537 3780 1.097547 GCTTCCACACCGGATCCATG 61.098 60.000 9.46 11.91 45.80 3.66
2538 3781 1.224592 GCTTCCACACCGGATCCAT 59.775 57.895 9.46 0.00 45.80 3.41
2545 3816 1.566018 GGTTCGAAGCTTCCACACCG 61.566 60.000 20.62 8.71 0.00 4.94
2577 3848 0.458197 CTCTCAGGCTCAAGTGCTCG 60.458 60.000 0.00 0.00 0.00 5.03
2579 3850 1.296068 GCTCTCAGGCTCAAGTGCT 59.704 57.895 11.32 0.00 0.00 4.40
2582 3853 1.910772 ACCGCTCTCAGGCTCAAGT 60.911 57.895 0.00 0.00 0.00 3.16
2591 3862 3.315142 GATGGCCACACCGCTCTCA 62.315 63.158 8.16 0.00 43.94 3.27
2617 3888 0.651551 GTCGCTCATCTAGTCGACGT 59.348 55.000 10.46 1.19 41.43 4.34
2625 3896 2.479560 CGATGGTGTTGTCGCTCATCTA 60.480 50.000 0.00 0.00 33.68 1.98
2630 3901 2.740714 GCCGATGGTGTTGTCGCTC 61.741 63.158 0.00 0.00 36.57 5.03
2631 3902 2.742372 GCCGATGGTGTTGTCGCT 60.742 61.111 0.00 0.00 36.57 4.93
2632 3903 2.398554 ATGCCGATGGTGTTGTCGC 61.399 57.895 0.00 0.00 36.57 5.19
2633 3904 1.018752 TCATGCCGATGGTGTTGTCG 61.019 55.000 0.00 0.00 37.58 4.35
2636 3907 0.677731 ACCTCATGCCGATGGTGTTG 60.678 55.000 0.00 0.00 0.00 3.33
2637 3908 0.677731 CACCTCATGCCGATGGTGTT 60.678 55.000 0.00 0.00 43.41 3.32
2638 3909 1.078214 CACCTCATGCCGATGGTGT 60.078 57.895 0.00 0.00 43.41 4.16
2641 3912 1.820906 CACCACCTCATGCCGATGG 60.821 63.158 4.21 4.21 36.46 3.51
2642 3913 2.475466 GCACCACCTCATGCCGATG 61.475 63.158 0.00 0.00 35.73 3.84
2643 3914 2.124570 GCACCACCTCATGCCGAT 60.125 61.111 0.00 0.00 35.73 4.18
2644 3915 3.189376 TTGCACCACCTCATGCCGA 62.189 57.895 0.00 0.00 41.33 5.54
2645 3916 2.672651 TTGCACCACCTCATGCCG 60.673 61.111 0.00 0.00 41.33 5.69
2646 3917 2.345760 CCTTGCACCACCTCATGCC 61.346 63.158 0.00 0.00 41.33 4.40
2647 3918 2.345760 CCCTTGCACCACCTCATGC 61.346 63.158 0.00 0.00 42.40 4.06
2648 3919 1.679977 CCCCTTGCACCACCTCATG 60.680 63.158 0.00 0.00 0.00 3.07
2649 3920 1.852157 TCCCCTTGCACCACCTCAT 60.852 57.895 0.00 0.00 0.00 2.90
2650 3921 2.449518 TCCCCTTGCACCACCTCA 60.450 61.111 0.00 0.00 0.00 3.86
2651 3922 2.034221 GTCCCCTTGCACCACCTC 59.966 66.667 0.00 0.00 0.00 3.85
2652 3923 3.953775 CGTCCCCTTGCACCACCT 61.954 66.667 0.00 0.00 0.00 4.00
2653 3924 3.268103 ATCGTCCCCTTGCACCACC 62.268 63.158 0.00 0.00 0.00 4.61
2661 3932 0.976073 ACGGATGACATCGTCCCCTT 60.976 55.000 13.45 0.00 46.80 3.95
2668 3939 1.000163 CTTCCCCTACGGATGACATCG 60.000 57.143 9.31 7.41 41.63 3.84
2673 3944 0.256752 TCGTCTTCCCCTACGGATGA 59.743 55.000 0.00 0.00 41.63 2.92
2675 3946 1.108132 GCTCGTCTTCCCCTACGGAT 61.108 60.000 0.00 0.00 41.63 4.18
2678 3949 1.139095 GTGCTCGTCTTCCCCTACG 59.861 63.158 0.00 0.00 40.40 3.51
2690 3961 2.667536 ACTGCTGCTTGGTGCTCG 60.668 61.111 0.00 0.00 43.37 5.03
2691 3962 1.598962 TCACTGCTGCTTGGTGCTC 60.599 57.895 0.00 0.00 43.37 4.26
2710 3981 2.829914 TATCCCGTCCCCACGTCG 60.830 66.667 0.00 0.00 45.17 5.12
2712 3983 0.906282 AAACTATCCCGTCCCCACGT 60.906 55.000 0.00 0.00 45.17 4.49
2714 3985 0.616891 ACAAACTATCCCGTCCCCAC 59.383 55.000 0.00 0.00 0.00 4.61
2723 3994 1.305219 TGCTGCCGCACAAACTATCC 61.305 55.000 0.00 0.00 42.25 2.59
2753 4024 1.079256 CTCCTCCCCCAGTCAGTCA 59.921 63.158 0.00 0.00 0.00 3.41
2810 4081 2.048023 CATCCACCACCAGCGCATT 61.048 57.895 11.47 0.00 0.00 3.56
2812 4083 3.952508 ACATCCACCACCAGCGCA 61.953 61.111 11.47 0.00 0.00 6.09
2816 4087 0.955428 CCGAACACATCCACCACCAG 60.955 60.000 0.00 0.00 0.00 4.00
2834 4105 6.503944 TCATTATATCTCTTCTCCCCTACCC 58.496 44.000 0.00 0.00 0.00 3.69
2877 4149 1.347707 TCTTTCCTCACATGCCTCGTT 59.652 47.619 0.00 0.00 0.00 3.85
2881 4153 3.795688 TTTCTCTTTCCTCACATGCCT 57.204 42.857 0.00 0.00 0.00 4.75
2930 4202 6.510879 AAATTTCGTCCTAATCCTGGTTTC 57.489 37.500 0.00 0.00 0.00 2.78
2952 4224 7.425606 GTCCTTCAAGTTTCAAAAGCAGATAA 58.574 34.615 0.00 0.00 0.00 1.75
2953 4225 6.293407 CGTCCTTCAAGTTTCAAAAGCAGATA 60.293 38.462 0.00 0.00 0.00 1.98
2955 4227 4.201910 CGTCCTTCAAGTTTCAAAAGCAGA 60.202 41.667 0.00 0.00 0.00 4.26
2958 4230 4.287238 TCGTCCTTCAAGTTTCAAAAGC 57.713 40.909 0.00 0.00 0.00 3.51
2963 4235 6.594159 GGAGATATTTCGTCCTTCAAGTTTCA 59.406 38.462 0.00 0.00 0.00 2.69
2996 4268 9.367160 CCAAAAGTATATATTTGGTCCCTCAAT 57.633 33.333 15.48 0.00 46.73 2.57
3065 4338 4.891992 TCCTGGTGAGGAAACTTTCTAG 57.108 45.455 1.57 0.00 46.19 2.43
3185 4462 6.975196 ATGCCCAGTTTGCACATTATATAA 57.025 33.333 0.00 0.00 42.38 0.98
3322 4870 4.647611 TGACACCGGAAATCATTAACACT 58.352 39.130 9.46 0.00 0.00 3.55
3329 4878 3.486383 ACAACTTGACACCGGAAATCAT 58.514 40.909 9.46 0.00 0.00 2.45
3358 4907 9.956720 AAAATGAACAACAGAAGTTATCTTGAG 57.043 29.630 0.00 0.00 35.73 3.02
3473 5073 6.725246 ACACGTAATCATTTAATGCTAAGCC 58.275 36.000 0.00 0.00 0.00 4.35
3528 5131 5.524281 GGAGGATCAGAGATTTTAACCGAAC 59.476 44.000 0.00 0.00 36.25 3.95
3531 5134 5.023533 TGGAGGATCAGAGATTTTAACCG 57.976 43.478 0.00 0.00 36.25 4.44
3903 5561 5.395642 GTGAGGAAAGAACAACGACAAAAA 58.604 37.500 0.00 0.00 0.00 1.94
3910 5568 2.561569 ACAGGTGAGGAAAGAACAACG 58.438 47.619 0.00 0.00 0.00 4.10
4389 6134 5.652014 CAGTTGTGCCCTTATTTGAATCCTA 59.348 40.000 0.00 0.00 0.00 2.94
4446 6200 4.646945 TGTGAATTCAGTTTTACCCAAGCA 59.353 37.500 8.80 0.00 0.00 3.91
4447 6201 4.982295 GTGTGAATTCAGTTTTACCCAAGC 59.018 41.667 8.80 0.00 0.00 4.01
4719 6475 8.287439 TGGAGTCAAGTTTTATGAACTTTCAA 57.713 30.769 6.37 0.00 41.13 2.69
4736 6492 3.806949 ATTAGGTTTGCCTGGAGTCAA 57.193 42.857 0.00 0.00 46.47 3.18
4743 6499 4.202441 ACTCTGCATATTAGGTTTGCCTG 58.798 43.478 0.00 0.00 46.47 4.85
4775 6531 3.567397 GGAGCTATTCACACTCCCTCTA 58.433 50.000 0.00 0.00 43.54 2.43
4787 6543 5.036117 TCCATACCAAACTGGAGCTATTC 57.964 43.478 0.00 0.00 40.96 1.75
4792 6548 2.092429 TGGATCCATACCAAACTGGAGC 60.092 50.000 11.44 0.00 44.45 4.70
4827 6583 2.666317 TGGGCTGATCGAGATGACTTA 58.334 47.619 0.00 0.00 0.00 2.24
4921 6677 4.200874 TCACCCACTTCGTAAAACATTGT 58.799 39.130 0.00 0.00 0.00 2.71
5043 6822 0.095935 CAGATGCGCTCACTTTTCCG 59.904 55.000 9.73 0.00 0.00 4.30
5077 6861 1.407989 GCAGCCTAGCCTGAAGACAAT 60.408 52.381 4.58 0.00 34.77 2.71
5203 6988 3.304928 GCTGGAAAACCTTCACAGACATG 60.305 47.826 0.00 0.00 34.39 3.21
5212 6997 0.247460 GCCATGGCTGGAAAACCTTC 59.753 55.000 29.98 0.00 46.37 3.46
5235 7020 6.741109 TCCGCACTCGATATAACTGAATTTA 58.259 36.000 0.00 0.00 38.10 1.40
5249 7034 0.320374 ATTCCTGTTTCCGCACTCGA 59.680 50.000 0.00 0.00 38.10 4.04
5250 7035 0.721718 GATTCCTGTTTCCGCACTCG 59.278 55.000 0.00 0.00 0.00 4.18
5253 7038 1.734465 CAGAGATTCCTGTTTCCGCAC 59.266 52.381 0.00 0.00 0.00 5.34
5258 7043 6.348868 GGAATGTTCACAGAGATTCCTGTTTC 60.349 42.308 0.00 6.59 44.32 2.78
5264 7049 5.496133 CATGGAATGTTCACAGAGATTCC 57.504 43.478 0.00 0.00 42.88 3.01
5313 7098 1.552337 TCCATCTTCTGACTGCTCACC 59.448 52.381 0.00 0.00 0.00 4.02
5322 7107 7.121315 CCGTAGTATACATGATCCATCTTCTGA 59.879 40.741 5.50 0.00 43.24 3.27
5325 7110 7.337184 TCTCCGTAGTATACATGATCCATCTTC 59.663 40.741 5.50 0.00 43.24 2.87
5330 7115 7.399634 TGTATCTCCGTAGTATACATGATCCA 58.600 38.462 5.50 0.00 43.24 3.41
5331 7116 7.860918 TGTATCTCCGTAGTATACATGATCC 57.139 40.000 5.50 0.00 43.24 3.36
5342 7127 3.887352 TGCTCTCTTGTATCTCCGTAGT 58.113 45.455 0.00 0.00 0.00 2.73
5344 7129 5.592054 CAAATGCTCTCTTGTATCTCCGTA 58.408 41.667 0.00 0.00 0.00 4.02
5346 7131 3.247173 GCAAATGCTCTCTTGTATCTCCG 59.753 47.826 0.00 0.00 38.21 4.63
5387 7172 0.754472 ACAAGAGTTTCGTTCCCGGA 59.246 50.000 0.73 0.00 33.95 5.14
5425 7211 6.425114 CCGGTAGTGAATCTCATCATTTTAGG 59.575 42.308 0.00 0.00 0.00 2.69
5435 7221 2.223735 GCGATTCCGGTAGTGAATCTCA 60.224 50.000 0.00 0.00 43.76 3.27
5579 7365 1.143183 GGCCTTTCTATGCCGACGA 59.857 57.895 0.00 0.00 38.00 4.20
5609 7395 0.663688 CGGACACAGTCGAGATAGGG 59.336 60.000 0.00 0.00 32.65 3.53
5616 7402 1.817357 AGATGTACGGACACAGTCGA 58.183 50.000 0.33 0.00 38.76 4.20
5621 7407 1.066454 CGGCATAGATGTACGGACACA 59.934 52.381 0.33 0.00 38.76 3.72
5653 7439 4.637970 GCGATAACGTTGCCGAAC 57.362 55.556 22.33 7.03 41.98 3.95
5706 7492 3.842126 CATGCCACGTGACGAGCG 61.842 66.667 19.30 0.00 33.92 5.03
5743 7634 4.882447 CTTAGTTTGAAACTATGCCGACG 58.118 43.478 17.54 0.00 43.09 5.12
5807 7698 1.073897 GCTCCAAGAGTGCCCAGTT 59.926 57.895 0.00 0.00 31.39 3.16
5814 7705 2.741228 GCATAGACCTGCTCCAAGAGTG 60.741 54.545 0.00 0.00 39.12 3.51
5815 7706 1.484240 GCATAGACCTGCTCCAAGAGT 59.516 52.381 0.00 0.00 39.12 3.24
5819 7710 0.975556 TCGGCATAGACCTGCTCCAA 60.976 55.000 0.00 0.00 41.95 3.53
5907 7798 2.203832 TGAGCTCCCAGTGGCTGA 60.204 61.111 12.15 0.00 39.05 4.26
5929 7820 1.134670 AGACAGAAACTATGCCGAGCC 60.135 52.381 0.00 0.00 0.00 4.70
6001 7914 6.497437 TGCATATATTTGTTGTGTGATGCTC 58.503 36.000 0.00 0.00 39.30 4.26
6045 7958 4.652421 TGAATTTGTTGTGTGATGCTGT 57.348 36.364 0.00 0.00 0.00 4.40
6102 8015 6.128172 GCTTGGTGGTGATGATACTTATATGC 60.128 42.308 0.00 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.