Multiple sequence alignment - TraesCS7D01G348300

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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 TraesCS7D01G348300 chr7D 100.000 7385 0 0 1 7385 447897294 447904678 0.000000e+00 13638.0
1 TraesCS7D01G348300 chr7D 80.000 105 16 4 6277 6379 123052137 123052238 1.030000e-08 73.1
2 TraesCS7D01G348300 chr7D 91.489 47 4 0 4578 4624 468819942 468819896 1.720000e-06 65.8
3 TraesCS7D01G348300 chr7D 97.297 37 1 0 3749 3785 332700587 332700551 6.190000e-06 63.9
4 TraesCS7D01G348300 chr7B 96.734 2909 60 11 2514 5407 465159351 465162239 0.000000e+00 4813.0
5 TraesCS7D01G348300 chr7B 93.520 2392 93 19 1 2353 465156990 465159358 0.000000e+00 3502.0
6 TraesCS7D01G348300 chr7B 94.815 1273 42 7 5831 7085 465162829 465164095 0.000000e+00 1964.0
7 TraesCS7D01G348300 chr7B 98.834 429 5 0 5406 5834 465162321 465162749 0.000000e+00 765.0
8 TraesCS7D01G348300 chr7B 92.055 365 9 1 1814 2158 344310927 344311291 5.150000e-136 496.0
9 TraesCS7D01G348300 chr7B 91.530 366 11 1 1813 2158 292831518 292831883 3.100000e-133 486.0
10 TraesCS7D01G348300 chr7B 92.760 221 12 3 7168 7385 465164095 465164314 4.300000e-82 316.0
11 TraesCS7D01G348300 chr7B 95.349 86 4 0 7087 7172 695952671 695952586 3.590000e-28 137.0
12 TraesCS7D01G348300 chr7B 82.443 131 12 10 5067 5196 2130085 2130205 3.640000e-18 104.0
13 TraesCS7D01G348300 chr7B 97.297 37 1 0 3749 3785 284964636 284964600 6.190000e-06 63.9
14 TraesCS7D01G348300 chr7A 93.095 3099 161 29 2157 5237 547768997 547765934 0.000000e+00 4488.0
15 TraesCS7D01G348300 chr7A 88.889 1521 106 35 5361 6840 547765623 547764125 0.000000e+00 1814.0
16 TraesCS7D01G348300 chr7A 91.995 762 36 13 1059 1812 547769723 547768979 0.000000e+00 1046.0
17 TraesCS7D01G348300 chr7A 94.340 106 6 0 7280 7385 547758999 547758894 5.930000e-36 163.0
18 TraesCS7D01G348300 chr7A 85.366 123 13 4 5067 5187 38729772 38729891 1.010000e-23 122.0
19 TraesCS7D01G348300 chr7A 85.859 99 13 1 2368 2466 634337835 634337738 3.640000e-18 104.0
20 TraesCS7D01G348300 chr7A 97.727 44 1 0 963 1006 547769823 547769780 7.950000e-10 76.8
21 TraesCS7D01G348300 chr7A 97.297 37 1 0 3749 3785 369474395 369474359 6.190000e-06 63.9
22 TraesCS7D01G348300 chr5B 92.033 364 7 3 1821 2163 222365789 222365427 6.660000e-135 492.0
23 TraesCS7D01G348300 chr5B 91.389 360 9 6 1821 2159 276248810 276249168 2.410000e-129 473.0
24 TraesCS7D01G348300 chr5B 94.382 89 5 0 7087 7175 603648295 603648383 3.590000e-28 137.0
25 TraesCS7D01G348300 chr5B 90.722 97 7 2 7087 7181 30585835 30585931 2.160000e-25 128.0
26 TraesCS7D01G348300 chr5B 87.500 112 10 2 7059 7169 105774118 105774010 7.780000e-25 126.0
27 TraesCS7D01G348300 chr5B 91.892 74 6 0 5067 5140 691225520 691225593 3.640000e-18 104.0
28 TraesCS7D01G348300 chr3B 91.622 370 8 4 1812 2158 39816311 39815942 2.390000e-134 490.0
29 TraesCS7D01G348300 chr3B 91.667 360 9 3 1821 2159 22779783 22780142 5.180000e-131 479.0
30 TraesCS7D01G348300 chr3B 90.186 377 12 5 1797 2152 603604869 603604497 1.120000e-127 468.0
31 TraesCS7D01G348300 chr3B 84.848 99 14 1 2368 2466 235829598 235829501 1.700000e-16 99.0
32 TraesCS7D01G348300 chr1B 91.989 362 8 6 1818 2159 478710509 478710869 8.610000e-134 488.0
33 TraesCS7D01G348300 chr1B 91.899 358 8 2 1822 2158 456733691 456733334 1.440000e-131 481.0
34 TraesCS7D01G348300 chr6B 91.304 368 12 7 1813 2160 125642123 125641756 1.110000e-132 484.0
35 TraesCS7D01G348300 chr6B 92.473 93 5 2 7087 7178 8774957 8775048 1.670000e-26 132.0
36 TraesCS7D01G348300 chr6B 90.816 98 8 1 7087 7184 574464813 574464717 6.010000e-26 130.0
37 TraesCS7D01G348300 chr6B 85.859 99 13 1 2368 2466 641881014 641880917 3.640000e-18 104.0
38 TraesCS7D01G348300 chr2D 92.135 356 8 1 1826 2161 402239437 402239082 1.110000e-132 484.0
39 TraesCS7D01G348300 chr2D 92.068 353 8 1 1826 2158 295166359 295166007 5.180000e-131 479.0
40 TraesCS7D01G348300 chr2D 88.889 108 10 2 7087 7193 567672295 567672189 1.670000e-26 132.0
41 TraesCS7D01G348300 chr2D 85.321 109 15 1 4532 4639 88082894 88082786 2.180000e-20 111.0
42 TraesCS7D01G348300 chr3D 91.877 357 8 2 1823 2158 526277891 526278247 5.180000e-131 479.0
43 TraesCS7D01G348300 chr3D 91.061 358 11 2 1828 2165 263802809 263802453 1.450000e-126 464.0
44 TraesCS7D01G348300 chr3D 95.294 85 4 0 7087 7171 611167339 611167255 1.290000e-27 135.0
45 TraesCS7D01G348300 chr3D 86.441 59 8 0 4565 4623 336537923 336537981 1.720000e-06 65.8
46 TraesCS7D01G348300 chr2B 91.620 358 9 3 1823 2159 551643183 551643540 6.700000e-130 475.0
47 TraesCS7D01G348300 chr4B 90.934 364 13 1 1815 2158 302734491 302734854 8.670000e-129 472.0
48 TraesCS7D01G348300 chr6A 96.386 83 3 0 7087 7169 219477782 219477864 3.590000e-28 137.0
49 TraesCS7D01G348300 chr6A 95.238 84 4 0 7087 7170 61182113 61182196 4.650000e-27 134.0
50 TraesCS7D01G348300 chr6A 93.182 88 6 0 7082 7169 15325185 15325272 6.010000e-26 130.0
51 TraesCS7D01G348300 chr6A 88.525 61 6 1 5068 5128 121627863 121627804 1.030000e-08 73.1
52 TraesCS7D01G348300 chr6A 90.385 52 3 2 5065 5115 21926929 21926879 4.780000e-07 67.6
53 TraesCS7D01G348300 chr6A 97.368 38 1 0 3749 3786 570921361 570921324 1.720000e-06 65.8
54 TraesCS7D01G348300 chr5D 94.382 89 5 0 7082 7170 135711778 135711690 3.590000e-28 137.0
55 TraesCS7D01G348300 chr5D 94.253 87 5 0 7087 7173 401281318 401281232 4.650000e-27 134.0
56 TraesCS7D01G348300 chr5D 94.253 87 5 0 7087 7173 423845948 423845862 4.650000e-27 134.0
57 TraesCS7D01G348300 chr5D 94.872 39 2 0 4587 4625 563971406 563971444 2.220000e-05 62.1
58 TraesCS7D01G348300 chr4D 96.386 83 3 0 7087 7169 301528643 301528725 3.590000e-28 137.0
59 TraesCS7D01G348300 chr4D 95.181 83 4 0 7087 7169 80976544 80976626 1.670000e-26 132.0
60 TraesCS7D01G348300 chr4D 93.258 89 6 0 7087 7175 102387003 102387091 1.670000e-26 132.0
61 TraesCS7D01G348300 chr4D 93.976 83 5 0 7087 7169 35618692 35618774 7.780000e-25 126.0
62 TraesCS7D01G348300 chr4D 93.023 86 6 0 7087 7172 447129515 447129600 7.780000e-25 126.0
63 TraesCS7D01G348300 chr4D 88.235 102 10 2 7087 7188 215187787 215187688 3.620000e-23 121.0
64 TraesCS7D01G348300 chr4A 96.386 83 3 0 7087 7169 547197780 547197698 3.590000e-28 137.0
65 TraesCS7D01G348300 chr4A 94.253 87 5 0 7087 7173 603715478 603715564 4.650000e-27 134.0
66 TraesCS7D01G348300 chr4A 82.443 131 17 5 5067 5196 642693384 642693259 7.830000e-20 110.0
67 TraesCS7D01G348300 chr5A 95.238 84 4 0 7087 7170 306880889 306880972 4.650000e-27 134.0
68 TraesCS7D01G348300 chrUn 95.181 83 4 0 7087 7169 325927185 325927267 1.670000e-26 132.0
69 TraesCS7D01G348300 chrUn 95.122 82 4 0 7091 7172 229545910 229545829 6.010000e-26 130.0
70 TraesCS7D01G348300 chrUn 94.048 84 5 0 7087 7170 226012889 226012806 2.160000e-25 128.0
71 TraesCS7D01G348300 chrUn 93.976 83 5 0 7087 7169 27602568 27602650 7.780000e-25 126.0
72 TraesCS7D01G348300 chrUn 92.941 85 6 0 7087 7171 316201941 316201857 2.800000e-24 124.0
73 TraesCS7D01G348300 chrUn 92.771 83 6 0 7087 7169 94863197 94863115 3.620000e-23 121.0
74 TraesCS7D01G348300 chrUn 92.771 83 6 0 7087 7169 226884327 226884245 3.620000e-23 121.0
75 TraesCS7D01G348300 chrUn 92.771 83 6 0 7087 7169 244923894 244923812 3.620000e-23 121.0
76 TraesCS7D01G348300 chrUn 92.771 83 6 0 7087 7169 258641821 258641903 3.620000e-23 121.0
77 TraesCS7D01G348300 chrUn 90.110 91 9 0 7087 7177 82171778 82171868 1.300000e-22 119.0
78 TraesCS7D01G348300 chrUn 88.542 96 11 0 7081 7176 55723608 55723703 4.680000e-22 117.0
79 TraesCS7D01G348300 chrUn 87.255 102 11 2 7087 7188 96524772 96524673 1.680000e-21 115.0
80 TraesCS7D01G348300 chr6D 93.258 89 6 0 7087 7175 229430745 229430657 1.670000e-26 132.0
81 TraesCS7D01G348300 chr6D 92.222 90 7 0 7087 7176 271233445 271233534 2.160000e-25 128.0
82 TraesCS7D01G348300 chr6D 92.135 89 7 0 7087 7175 142141164 142141252 7.780000e-25 126.0
83 TraesCS7D01G348300 chr6D 92.771 83 6 0 7087 7169 291718571 291718653 3.620000e-23 121.0
84 TraesCS7D01G348300 chr6D 100.000 38 0 0 3749 3786 426058452 426058415 3.700000e-08 71.3
85 TraesCS7D01G348300 chr1A 94.186 86 5 0 7087 7172 107663277 107663192 1.670000e-26 132.0
86 TraesCS7D01G348300 chr1A 96.250 80 3 0 7090 7169 345300409 345300330 1.670000e-26 132.0
87 TraesCS7D01G348300 chr1A 93.258 89 6 0 7087 7175 589793250 589793162 1.670000e-26 132.0
88 TraesCS7D01G348300 chr1A 90.099 101 9 1 7071 7170 578487946 578487846 6.010000e-26 130.0
89 TraesCS7D01G348300 chr1A 87.209 86 11 0 4538 4623 63517933 63517848 1.700000e-16 99.0
90 TraesCS7D01G348300 chr1D 93.103 87 6 0 7087 7173 348120776 348120862 2.160000e-25 128.0
91 TraesCS7D01G348300 chr1D 93.023 86 6 0 7084 7169 12546922 12547007 7.780000e-25 126.0
92 TraesCS7D01G348300 chr1D 92.135 89 7 0 7087 7175 124331988 124331900 7.780000e-25 126.0
93 TraesCS7D01G348300 chr1D 91.398 93 7 1 7079 7170 465077620 465077528 7.780000e-25 126.0
94 TraesCS7D01G348300 chr1D 92.045 88 7 0 7087 7174 233353185 233353098 2.800000e-24 124.0
95 TraesCS7D01G348300 chr3A 84.848 99 14 1 2368 2466 621623391 621623488 1.700000e-16 99.0
96 TraesCS7D01G348300 chr3A 84.746 59 9 0 4565 4623 453819376 453819434 8.000000e-05 60.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G348300 chr7D 447897294 447904678 7384 False 13638.0 13638 100.0000 1 7385 1 chr7D.!!$F2 7384
1 TraesCS7D01G348300 chr7B 465156990 465164314 7324 False 2272.0 4813 95.3326 1 7385 5 chr7B.!!$F4 7384
2 TraesCS7D01G348300 chr7A 547764125 547769823 5698 True 1856.2 4488 92.9265 963 6840 4 chr7A.!!$R4 5877

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
180 181 0.182775 AAGGGTGGGTGACTGACAAC 59.817 55.000 0.00 0.0 35.09 3.32 F
386 387 0.320421 GGTGTTGGCGAGCAAGTCTA 60.320 55.000 0.00 0.0 0.00 2.59 F
390 391 0.673644 TTGGCGAGCAAGTCTAAGGC 60.674 55.000 0.00 0.0 0.00 4.35 F
1922 1987 0.541863 CACCCATCCCAGTACCACTC 59.458 60.000 0.00 0.0 0.00 3.51 F
2166 2231 0.391130 TAGGCGGAGTTGATGTGTGC 60.391 55.000 0.00 0.0 0.00 4.57 F
4003 4083 0.320858 TCGCCAAGTCGCCATGTTTA 60.321 50.000 0.00 0.0 0.00 2.01 F
4159 4239 3.691118 TCAGCATGTGCCTATTTGACTTC 59.309 43.478 0.57 0.0 43.38 3.01 F
5259 5359 1.746615 GCTGCATCCGTGGTCACAT 60.747 57.895 0.00 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 1383 0.106519 CATCCCCCTCATGGACAACC 60.107 60.000 0.00 0.0 33.94 3.77 R
1912 1977 0.320374 TTTGGGCGAGAGTGGTACTG 59.680 55.000 0.00 0.0 0.00 2.74 R
1988 2053 1.279271 CCTGGGAAGTCCTCGTGAAAT 59.721 52.381 0.00 0.0 36.20 2.17 R
3105 3172 5.451103 GCAGAAATATTCCTCCTCAAAAGGC 60.451 44.000 0.00 0.0 43.02 4.35 R
4139 4219 3.960571 AGAAGTCAAATAGGCACATGCT 58.039 40.909 3.48 0.0 41.70 3.79 R
5059 5149 1.576421 GAGTTCCAACAAGCAGGCG 59.424 57.895 0.00 0.0 0.00 5.52 R
5281 5383 1.933021 AGGTCGGTTCAGGTCATGTA 58.067 50.000 0.00 0.0 0.00 2.29 R
7012 7573 0.602638 TGCTGTGCGGGTAGAAACTG 60.603 55.000 0.00 0.0 0.00 3.16 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
29 30 1.803289 TCGAGATGCGAGGAGTGTG 59.197 57.895 0.00 0.00 45.59 3.82
86 87 2.030893 CACAATGCATGAACCTTGACGT 60.031 45.455 0.00 0.00 0.00 4.34
136 137 5.664457 TCAGAATGACTCGATATGCAAGTT 58.336 37.500 0.00 0.00 42.56 2.66
138 139 7.264947 TCAGAATGACTCGATATGCAAGTTAA 58.735 34.615 0.00 0.00 42.56 2.01
168 169 2.362889 GCATGGGTGGAAGGGTGG 60.363 66.667 0.00 0.00 0.00 4.61
176 177 1.074090 TGGAAGGGTGGGTGACTGA 60.074 57.895 0.00 0.00 0.00 3.41
180 181 0.182775 AAGGGTGGGTGACTGACAAC 59.817 55.000 0.00 0.00 35.09 3.32
200 201 1.443407 CCGGTCTGAATCAGGCGAT 59.557 57.895 10.71 0.00 36.90 4.58
223 224 6.041423 TGATGTTCTGTTGCAGATAGAAGA 57.959 37.500 8.93 8.60 40.39 2.87
224 225 6.647229 TGATGTTCTGTTGCAGATAGAAGAT 58.353 36.000 14.73 14.73 40.58 2.40
234 235 9.617523 TGTTGCAGATAGAAGATATCATTCAAA 57.382 29.630 5.32 0.35 0.00 2.69
256 257 5.722172 ATCATAGATATGGTCAATGGGGG 57.278 43.478 0.19 0.00 34.50 5.40
257 258 3.266772 TCATAGATATGGTCAATGGGGGC 59.733 47.826 0.19 0.00 34.50 5.80
258 259 1.533187 AGATATGGTCAATGGGGGCA 58.467 50.000 0.00 0.00 0.00 5.36
309 310 4.447290 TGTTTTCTCTCGTCATTGTTCCA 58.553 39.130 0.00 0.00 0.00 3.53
313 314 2.095212 TCTCTCGTCATTGTTCCAGTCG 60.095 50.000 0.00 0.00 0.00 4.18
386 387 0.320421 GGTGTTGGCGAGCAAGTCTA 60.320 55.000 0.00 0.00 0.00 2.59
390 391 0.673644 TTGGCGAGCAAGTCTAAGGC 60.674 55.000 0.00 0.00 0.00 4.35
416 417 2.884639 AGTTTGGCTTTGCAACGACTAT 59.115 40.909 10.48 0.00 0.00 2.12
428 429 6.964807 TGCAACGACTATAAACCCTATAGA 57.035 37.500 0.00 0.00 33.10 1.98
449 450 2.288025 GGGCACTTGGGACTCCGTA 61.288 63.158 0.00 0.00 35.24 4.02
497 498 8.754991 TTTGGGTCTTCAGTTTGACTAATAAA 57.245 30.769 0.00 0.00 34.01 1.40
559 560 9.859152 AAATTTAATTCAACCAAGGATCCAAAA 57.141 25.926 15.82 0.00 0.00 2.44
560 561 9.859152 AATTTAATTCAACCAAGGATCCAAAAA 57.141 25.926 15.82 0.00 0.00 1.94
602 618 9.180678 GTCAAATCGATGACTAAAAATTTGTGT 57.819 29.630 11.13 0.00 44.98 3.72
609 625 5.218885 TGACTAAAAATTTGTGTCGGCATG 58.781 37.500 0.00 0.00 31.95 4.06
642 658 6.942976 TGATAGAGGTTTTCGAGTTGGTATT 58.057 36.000 0.00 0.00 0.00 1.89
643 659 7.391620 TGATAGAGGTTTTCGAGTTGGTATTT 58.608 34.615 0.00 0.00 0.00 1.40
646 662 7.611213 AGAGGTTTTCGAGTTGGTATTTATG 57.389 36.000 0.00 0.00 0.00 1.90
652 668 5.209818 TCGAGTTGGTATTTATGGCTAGG 57.790 43.478 0.00 0.00 0.00 3.02
720 736 1.202592 GGTTGCGGTTGTTTTTCCCAT 60.203 47.619 0.00 0.00 0.00 4.00
745 761 6.862608 TCAATCAAGATTTTTCAATCGTGGTG 59.137 34.615 9.90 8.88 44.57 4.17
746 762 4.545610 TCAAGATTTTTCAATCGTGGTGC 58.454 39.130 9.90 0.00 44.57 5.01
747 763 4.278170 TCAAGATTTTTCAATCGTGGTGCT 59.722 37.500 9.90 0.00 44.57 4.40
751 767 3.347958 TTTTCAATCGTGGTGCTCAAC 57.652 42.857 0.00 0.00 0.00 3.18
752 768 6.574185 GATTTTTCAATCGTGGTGCTCAACC 61.574 44.000 0.00 0.00 38.31 3.77
832 848 2.489329 AGTGGGAGCGACATTTTCATTG 59.511 45.455 0.00 0.00 0.00 2.82
838 854 5.163663 GGGAGCGACATTTTCATTGATAACA 60.164 40.000 0.00 0.00 0.00 2.41
843 859 6.258160 CGACATTTTCATTGATAACAGGACC 58.742 40.000 0.00 0.00 0.00 4.46
844 860 6.530019 ACATTTTCATTGATAACAGGACCC 57.470 37.500 0.00 0.00 0.00 4.46
861 877 3.364549 GACCCCCATGATGATTTTGTCA 58.635 45.455 0.00 0.00 42.06 3.58
865 881 4.406326 CCCCCATGATGATTTTGTCAATCA 59.594 41.667 0.00 0.00 40.97 2.57
1330 1383 2.287547 CCCCGATTCGGTTATGCAATTG 60.288 50.000 22.83 0.00 46.80 2.32
1331 1384 2.287547 CCCGATTCGGTTATGCAATTGG 60.288 50.000 22.83 0.08 46.80 3.16
1332 1385 2.357637 CCGATTCGGTTATGCAATTGGT 59.642 45.455 17.08 0.00 42.73 3.67
1333 1386 3.181491 CCGATTCGGTTATGCAATTGGTT 60.181 43.478 17.08 0.00 42.73 3.67
1334 1387 3.790820 CGATTCGGTTATGCAATTGGTTG 59.209 43.478 7.72 0.00 38.39 3.77
1335 1388 4.674101 CGATTCGGTTATGCAATTGGTTGT 60.674 41.667 7.72 0.00 37.65 3.32
1336 1389 3.840890 TCGGTTATGCAATTGGTTGTC 57.159 42.857 7.72 0.00 37.65 3.18
1337 1390 2.490115 TCGGTTATGCAATTGGTTGTCC 59.510 45.455 7.72 0.00 37.65 4.02
1338 1391 2.230025 CGGTTATGCAATTGGTTGTCCA 59.770 45.455 7.72 0.00 42.66 4.02
1339 1392 3.119173 CGGTTATGCAATTGGTTGTCCAT 60.119 43.478 7.72 3.58 43.91 3.41
1340 1393 4.183101 GGTTATGCAATTGGTTGTCCATG 58.817 43.478 7.72 0.00 43.91 3.66
1341 1394 4.081752 GGTTATGCAATTGGTTGTCCATGA 60.082 41.667 7.72 0.00 43.91 3.07
1342 1395 3.880047 ATGCAATTGGTTGTCCATGAG 57.120 42.857 7.72 0.00 43.91 2.90
1343 1396 1.894466 TGCAATTGGTTGTCCATGAGG 59.106 47.619 7.72 0.00 43.91 3.86
1344 1397 1.205417 GCAATTGGTTGTCCATGAGGG 59.795 52.381 7.72 0.00 43.91 4.30
1567 1626 2.484889 AGGAAGAGCACGTGAGTTTTC 58.515 47.619 22.23 15.26 46.40 2.29
1815 1880 6.875948 TTTGATGTGTGCTGTACAATTACT 57.124 33.333 0.00 0.00 41.89 2.24
1819 1884 6.589907 TGATGTGTGCTGTACAATTACTACTG 59.410 38.462 0.00 0.00 41.89 2.74
1912 1977 2.378634 CCAGGAGGTCACCCATCCC 61.379 68.421 0.00 0.00 31.79 3.85
1917 1982 0.831307 GAGGTCACCCATCCCAGTAC 59.169 60.000 0.00 0.00 0.00 2.73
1918 1983 0.620700 AGGTCACCCATCCCAGTACC 60.621 60.000 0.00 0.00 0.00 3.34
1922 1987 0.541863 CACCCATCCCAGTACCACTC 59.458 60.000 0.00 0.00 0.00 3.51
1924 1989 1.123928 CCCATCCCAGTACCACTCTC 58.876 60.000 0.00 0.00 0.00 3.20
1988 2053 6.134535 ACACAACCCTTAGATATGAAACCA 57.865 37.500 0.00 0.00 0.00 3.67
2065 2130 2.241176 GGTTTCATACCCATGGGACTGA 59.759 50.000 38.07 30.96 41.43 3.41
2114 2179 4.141688 CCTATCACAACCCTCCTCCTTTAC 60.142 50.000 0.00 0.00 0.00 2.01
2160 2225 3.034635 AGAAGACATAGGCGGAGTTGAT 58.965 45.455 0.00 0.00 0.00 2.57
2166 2231 0.391130 TAGGCGGAGTTGATGTGTGC 60.391 55.000 0.00 0.00 0.00 4.57
2281 2346 5.710099 GGAAGGTTTGTTTCATCTATGGTCA 59.290 40.000 0.00 0.00 0.00 4.02
2352 2418 4.430007 GTGGATACTTCATGCACGTCTTA 58.570 43.478 0.00 0.00 44.69 2.10
2420 2486 0.610174 CTGAGCAACCACTAGAGGCA 59.390 55.000 6.07 0.00 0.00 4.75
2447 2513 7.944061 AGTTGTCATGAAAATTGATGAGTTGA 58.056 30.769 0.61 0.00 31.52 3.18
2460 2526 8.868522 ATTGATGAGTTGATTAAGAGGAACAA 57.131 30.769 0.00 0.00 0.00 2.83
2466 2532 7.226720 TGAGTTGATTAAGAGGAACAAACAGTC 59.773 37.037 0.00 0.00 0.00 3.51
2477 2543 4.276926 GGAACAAACAGTCAAGATCTGCTT 59.723 41.667 0.00 0.00 36.50 3.91
2673 2739 1.069049 ACAGGAAAACACCATGCAAGC 59.931 47.619 0.00 0.00 0.00 4.01
2848 2915 9.113876 GGTCAACTAATCACAAAGTTAATTTCG 57.886 33.333 0.00 0.00 34.23 3.46
2909 2976 2.293122 TGTGCAGCAAGTCCAAATGTAC 59.707 45.455 0.00 0.00 0.00 2.90
2993 3060 5.297569 AGTTACTCTTTGACCAGAAGCTT 57.702 39.130 0.00 0.00 0.00 3.74
3105 3172 4.002982 TGTTCCCTTTTCTCATCGATGTG 58.997 43.478 24.09 21.45 0.00 3.21
3416 3495 7.987458 CGCTATTATATATGGTGGATTGAAGGT 59.013 37.037 0.00 0.00 0.00 3.50
3662 3741 5.221880 CGGTGATGTTGTCATTTGATGTTT 58.778 37.500 0.00 0.00 39.48 2.83
3865 3944 5.123186 CCTTTACCGTTGATGCATCTGTTAA 59.877 40.000 26.32 15.81 0.00 2.01
4003 4083 0.320858 TCGCCAAGTCGCCATGTTTA 60.321 50.000 0.00 0.00 0.00 2.01
4139 4219 6.399743 TCGTGCACCTATATAACTTTGTTCA 58.600 36.000 12.15 0.00 0.00 3.18
4159 4239 3.691118 TCAGCATGTGCCTATTTGACTTC 59.309 43.478 0.57 0.00 43.38 3.01
4395 4475 7.634671 TGCACAATCAGATCATTTCAGTAAT 57.365 32.000 0.00 0.00 0.00 1.89
4503 4583 4.459685 CGTGGGTTTGGGTCATGTTATTTA 59.540 41.667 0.00 0.00 0.00 1.40
4567 4647 8.504811 TCTCCTATCCATATTAATTGTCACCA 57.495 34.615 0.00 0.00 0.00 4.17
4919 5000 6.336566 TGCACAAACACAAATTCTAACATGT 58.663 32.000 0.00 0.00 0.00 3.21
5045 5135 7.031226 TGATTTTCTAATGCTGCATACCTTC 57.969 36.000 16.58 7.53 0.00 3.46
5059 5149 2.639286 CTTCGTGTGCCTGTTGCC 59.361 61.111 0.00 0.00 40.16 4.52
5176 5267 6.483307 GTGCCTTTCTTTTGCCTCTTTATTTT 59.517 34.615 0.00 0.00 0.00 1.82
5177 5268 7.012327 GTGCCTTTCTTTTGCCTCTTTATTTTT 59.988 33.333 0.00 0.00 0.00 1.94
5178 5269 7.226523 TGCCTTTCTTTTGCCTCTTTATTTTTC 59.773 33.333 0.00 0.00 0.00 2.29
5179 5270 7.226523 GCCTTTCTTTTGCCTCTTTATTTTTCA 59.773 33.333 0.00 0.00 0.00 2.69
5180 5271 9.276590 CCTTTCTTTTGCCTCTTTATTTTTCAT 57.723 29.630 0.00 0.00 0.00 2.57
5259 5359 1.746615 GCTGCATCCGTGGTCACAT 60.747 57.895 0.00 0.00 0.00 3.21
5261 5361 1.811558 GCTGCATCCGTGGTCACATAT 60.812 52.381 0.00 0.00 0.00 1.78
5263 5363 3.866066 GCTGCATCCGTGGTCACATATAT 60.866 47.826 0.00 0.00 0.00 0.86
5265 5365 5.664457 CTGCATCCGTGGTCACATATATAT 58.336 41.667 1.90 0.00 0.00 0.86
5267 5367 7.360113 TGCATCCGTGGTCACATATATATAT 57.640 36.000 0.00 0.00 0.00 0.86
5335 5437 7.068061 CCCTAGACCTACTACAAATCCTAGTT 58.932 42.308 0.00 0.00 0.00 2.24
5459 5885 0.174845 TAGCCGGACCAATCGACTTG 59.825 55.000 5.05 0.00 34.42 3.16
5905 6415 4.963276 CATCGTTTATGCCTTTGGAGAA 57.037 40.909 0.00 0.00 0.00 2.87
6264 6806 7.119846 GTGTGAGCACTCAGTTTCCTATAATTT 59.880 37.037 0.00 0.00 40.75 1.82
6312 6854 2.949644 GTCAACTGGTAACTGCTTGGTT 59.050 45.455 0.00 0.00 39.52 3.67
6451 6994 8.846943 ATAAACCTTGAAAATGAAATGTTCCC 57.153 30.769 0.00 0.00 39.92 3.97
6531 7074 9.586435 GATTTTACAATGTCAATTAGAAAGGGG 57.414 33.333 0.00 0.00 0.00 4.79
6539 7082 4.889995 GTCAATTAGAAAGGGGAGGGATTG 59.110 45.833 0.00 0.00 0.00 2.67
6600 7143 2.440247 TCAGAGATGAGCCGCCGA 60.440 61.111 0.00 0.00 0.00 5.54
6642 7186 7.423844 TGAGAGATACAGAAGCTTTAATCCA 57.576 36.000 0.00 0.00 0.00 3.41
6662 7208 4.478317 TCCATGTAAAAGGTGGGAGATGAT 59.522 41.667 0.00 0.00 33.78 2.45
6684 7230 4.722526 TTCATTTCCCTGAAGACTTGGA 57.277 40.909 0.00 0.00 31.65 3.53
6810 7361 3.165071 AGCCAAGGTTTCAATTACCAGG 58.835 45.455 0.00 1.81 38.16 4.45
6823 7374 2.579624 TACCAGGGGCTCTCCAATAA 57.420 50.000 0.00 0.00 37.22 1.40
6833 7384 6.012745 GGGGCTCTCCAATAACATCATATTT 58.987 40.000 0.00 0.00 37.22 1.40
6834 7385 6.151817 GGGGCTCTCCAATAACATCATATTTC 59.848 42.308 0.00 0.00 37.22 2.17
6860 7411 2.817258 TCAGCCAAGGTTTCAATTACCG 59.183 45.455 0.00 0.00 40.69 4.02
6881 7432 0.179936 AGGCTCTCCAATAGCAGCAC 59.820 55.000 0.00 0.00 41.93 4.40
6906 7457 4.666412 TGGACATCCTTCCCATAACAAA 57.334 40.909 0.00 0.00 34.33 2.83
6912 7463 6.256053 ACATCCTTCCCATAACAAAACTGAT 58.744 36.000 0.00 0.00 0.00 2.90
6918 7469 7.546667 CCTTCCCATAACAAAACTGATTTCATG 59.453 37.037 0.00 0.00 0.00 3.07
6921 7472 8.814931 TCCCATAACAAAACTGATTTCATGATT 58.185 29.630 0.00 0.00 0.00 2.57
6938 7489 5.711506 TCATGATTGTTCTATTGCACCAGTT 59.288 36.000 0.00 0.00 0.00 3.16
6960 7511 2.757099 CCCCTCCATGGCTTGCAC 60.757 66.667 6.96 0.00 0.00 4.57
6971 7522 0.239347 GGCTTGCACAAGTAGCACTG 59.761 55.000 11.77 0.00 42.54 3.66
7002 7563 2.985456 CTCTTCTGCCGGCTTCCT 59.015 61.111 29.70 0.00 0.00 3.36
7012 7573 1.671328 GCCGGCTTCCTGATAACTTTC 59.329 52.381 22.15 0.00 0.00 2.62
7032 7598 0.320771 AGTTTCTACCCGCACAGCAG 60.321 55.000 0.00 0.00 0.00 4.24
7035 7601 2.125512 CTACCCGCACAGCAGGTC 60.126 66.667 0.00 0.00 38.77 3.85
7088 7654 6.889301 TCTATGATTTGCATGGATTTCCTC 57.111 37.500 0.00 0.00 39.27 3.71
7089 7655 4.950205 ATGATTTGCATGGATTTCCTCC 57.050 40.909 0.00 0.00 45.19 4.30
7090 7656 3.033184 TGATTTGCATGGATTTCCTCCC 58.967 45.455 0.00 0.00 44.23 4.30
7092 7658 2.442236 TTGCATGGATTTCCTCCCTC 57.558 50.000 0.00 0.00 44.23 4.30
7093 7659 0.552848 TGCATGGATTTCCTCCCTCC 59.447 55.000 0.00 0.00 44.23 4.30
7094 7660 0.536006 GCATGGATTTCCTCCCTCCG 60.536 60.000 0.00 0.00 44.23 4.63
7096 7662 2.047061 CATGGATTTCCTCCCTCCGTA 58.953 52.381 0.00 0.00 44.23 4.02
7097 7663 2.257391 TGGATTTCCTCCCTCCGTAA 57.743 50.000 0.00 0.00 44.23 3.18
7098 7664 2.553464 TGGATTTCCTCCCTCCGTAAA 58.447 47.619 0.00 0.00 44.23 2.01
7099 7665 2.237893 TGGATTTCCTCCCTCCGTAAAC 59.762 50.000 0.00 0.00 44.23 2.01
7100 7666 2.504585 GGATTTCCTCCCTCCGTAAACT 59.495 50.000 0.00 0.00 38.19 2.66
7101 7667 3.708121 GGATTTCCTCCCTCCGTAAACTA 59.292 47.826 0.00 0.00 38.19 2.24
7102 7668 4.162888 GGATTTCCTCCCTCCGTAAACTAA 59.837 45.833 0.00 0.00 38.19 2.24
7103 7669 5.163227 GGATTTCCTCCCTCCGTAAACTAAT 60.163 44.000 0.00 0.00 38.19 1.73
7104 7670 6.042437 GGATTTCCTCCCTCCGTAAACTAATA 59.958 42.308 0.00 0.00 38.19 0.98
7105 7671 7.256583 GGATTTCCTCCCTCCGTAAACTAATAT 60.257 40.741 0.00 0.00 38.19 1.28
7106 7672 8.731591 ATTTCCTCCCTCCGTAAACTAATATA 57.268 34.615 0.00 0.00 0.00 0.86
7107 7673 8.551682 TTTCCTCCCTCCGTAAACTAATATAA 57.448 34.615 0.00 0.00 0.00 0.98
7108 7674 7.771927 TCCTCCCTCCGTAAACTAATATAAG 57.228 40.000 0.00 0.00 0.00 1.73
7109 7675 7.529555 TCCTCCCTCCGTAAACTAATATAAGA 58.470 38.462 0.00 0.00 0.00 2.10
7110 7676 8.006564 TCCTCCCTCCGTAAACTAATATAAGAA 58.993 37.037 0.00 0.00 0.00 2.52
7111 7677 8.813951 CCTCCCTCCGTAAACTAATATAAGAAT 58.186 37.037 0.00 0.00 0.00 2.40
7112 7678 9.640963 CTCCCTCCGTAAACTAATATAAGAATG 57.359 37.037 0.00 0.00 0.00 2.67
7113 7679 9.151177 TCCCTCCGTAAACTAATATAAGAATGT 57.849 33.333 0.00 0.00 0.00 2.71
7114 7680 9.774413 CCCTCCGTAAACTAATATAAGAATGTT 57.226 33.333 0.00 0.00 0.00 2.71
7163 7729 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
7164 7730 8.461249 ACGCTCTTATATTAGTTTACAGAGGA 57.539 34.615 0.00 0.00 0.00 3.71
7165 7731 8.910944 ACGCTCTTATATTAGTTTACAGAGGAA 58.089 33.333 0.00 0.00 0.00 3.36
7166 7732 9.400638 CGCTCTTATATTAGTTTACAGAGGAAG 57.599 37.037 0.00 0.00 0.00 3.46
7271 7838 0.107831 CGACAAGAAGGTTGGGTCCA 59.892 55.000 0.00 0.00 0.00 4.02
7311 7878 1.950909 CAAAGGGTGAAGTTGCGGTAA 59.049 47.619 0.00 0.00 0.00 2.85
7335 7902 0.038709 AGCTCGAGATAATCCTGCGC 60.039 55.000 18.75 0.00 0.00 6.09
7342 7909 0.032130 GATAATCCTGCGCCGACTCA 59.968 55.000 4.18 0.00 0.00 3.41
7344 7911 1.600511 TAATCCTGCGCCGACTCACA 61.601 55.000 4.18 0.00 0.00 3.58
7355 7922 2.414824 GCCGACTCACAAAACAACACAA 60.415 45.455 0.00 0.00 0.00 3.33
7357 7924 3.606346 CCGACTCACAAAACAACACAAAC 59.394 43.478 0.00 0.00 0.00 2.93
7358 7925 3.606346 CGACTCACAAAACAACACAAACC 59.394 43.478 0.00 0.00 0.00 3.27
7363 7930 2.670414 ACAAAACAACACAAACCGCATG 59.330 40.909 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.166814 CGTTGCTGCTCTTTGGTAGC 59.833 55.000 0.00 0.00 43.47 3.58
62 63 3.004629 GTCAAGGTTCATGCATTGTGTCA 59.995 43.478 0.00 0.00 32.69 3.58
86 87 1.511850 CACCTCAATTGCGAGTGTGA 58.488 50.000 5.07 0.00 36.83 3.58
136 137 2.242196 CCCATGCTCCCTTCCTCTTTTA 59.758 50.000 0.00 0.00 0.00 1.52
138 139 0.627986 CCCATGCTCCCTTCCTCTTT 59.372 55.000 0.00 0.00 0.00 2.52
168 169 3.041940 CCGGCGTTGTCAGTCACC 61.042 66.667 6.01 0.00 0.00 4.02
176 177 0.670546 CTGATTCAGACCGGCGTTGT 60.671 55.000 8.00 0.00 32.44 3.32
180 181 2.892425 GCCTGATTCAGACCGGCG 60.892 66.667 15.36 0.00 32.44 6.46
200 201 6.041423 TCTTCTATCTGCAACAGAACATCA 57.959 37.500 0.74 0.00 44.04 3.07
234 235 4.079558 GCCCCCATTGACCATATCTATGAT 60.080 45.833 0.00 0.00 41.51 2.45
244 245 4.738998 CGCTGCCCCCATTGACCA 62.739 66.667 0.00 0.00 0.00 4.02
275 276 4.268359 GAGAGAAAACAATGGAGCAGGAT 58.732 43.478 0.00 0.00 0.00 3.24
329 330 1.442526 GCCAATCTCCTCATGCACCG 61.443 60.000 0.00 0.00 0.00 4.94
368 369 1.461127 CTTAGACTTGCTCGCCAACAC 59.539 52.381 0.00 0.00 0.00 3.32
428 429 2.539081 GGAGTCCCAAGTGCCCCTT 61.539 63.158 0.00 0.00 0.00 3.95
461 462 4.435137 TGAAGACCCAAAATCTCCCTCTA 58.565 43.478 0.00 0.00 0.00 2.43
562 563 8.826710 TCATCGATTTGACTAGCGAAATTAAAT 58.173 29.630 0.00 0.00 36.28 1.40
565 566 7.161829 GTCATCGATTTGACTAGCGAAATTA 57.838 36.000 11.13 0.00 42.22 1.40
566 567 6.037423 GTCATCGATTTGACTAGCGAAATT 57.963 37.500 11.13 0.00 42.22 1.82
567 568 5.643339 GTCATCGATTTGACTAGCGAAAT 57.357 39.130 11.13 0.00 42.22 2.17
602 618 0.327924 ATCAGGGTTTGTCATGCCGA 59.672 50.000 0.00 0.00 0.00 5.54
617 633 4.822026 ACCAACTCGAAAACCTCTATCAG 58.178 43.478 0.00 0.00 0.00 2.90
661 677 2.692741 CACCTCTTCCCCTCCCCC 60.693 72.222 0.00 0.00 0.00 5.40
669 685 1.004918 CACGGACACCACCTCTTCC 60.005 63.158 0.00 0.00 0.00 3.46
671 687 1.978455 TTGCACGGACACCACCTCTT 61.978 55.000 0.00 0.00 0.00 2.85
674 690 2.203153 GTTGCACGGACACCACCT 60.203 61.111 0.00 0.00 0.00 4.00
699 715 0.175989 GGGAAAAACAACCGCAACCA 59.824 50.000 0.00 0.00 0.00 3.67
701 717 2.131972 GATGGGAAAAACAACCGCAAC 58.868 47.619 0.00 0.00 0.00 4.17
720 736 6.862608 CACCACGATTGAAAAATCTTGATTGA 59.137 34.615 6.53 0.00 32.17 2.57
745 761 4.488879 GTTTTGATCCTTGATGGTTGAGC 58.511 43.478 0.00 0.00 37.07 4.26
746 762 4.082026 GGGTTTTGATCCTTGATGGTTGAG 60.082 45.833 0.00 0.00 37.07 3.02
747 763 3.831911 GGGTTTTGATCCTTGATGGTTGA 59.168 43.478 0.00 0.00 37.07 3.18
751 767 3.770933 ACATGGGTTTTGATCCTTGATGG 59.229 43.478 0.00 0.00 33.84 3.51
752 768 5.410355 AACATGGGTTTTGATCCTTGATG 57.590 39.130 0.00 0.00 31.83 3.07
755 771 4.990426 GTCAAACATGGGTTTTGATCCTTG 59.010 41.667 11.73 0.00 44.63 3.61
832 848 2.711009 TCATCATGGGGGTCCTGTTATC 59.289 50.000 0.00 0.00 0.00 1.75
838 854 2.315763 ACAAAATCATCATGGGGGTCCT 59.684 45.455 0.00 0.00 0.00 3.85
843 859 5.601583 TGATTGACAAAATCATCATGGGG 57.398 39.130 0.00 0.00 37.11 4.96
844 860 6.811954 TCATGATTGACAAAATCATCATGGG 58.188 36.000 20.62 5.02 43.38 4.00
861 877 4.260985 TCACGTGGCATAACTTCATGATT 58.739 39.130 17.00 0.00 0.00 2.57
865 881 4.009675 ACATTCACGTGGCATAACTTCAT 58.990 39.130 17.00 0.00 0.00 2.57
930 958 1.004044 ACTGCTCAGAATGGTTGAGGG 59.996 52.381 3.60 0.00 41.82 4.30
931 959 2.082231 CACTGCTCAGAATGGTTGAGG 58.918 52.381 3.60 0.00 41.82 3.86
933 961 1.699083 TCCACTGCTCAGAATGGTTGA 59.301 47.619 3.60 0.00 36.16 3.18
1013 1042 1.005450 GGTGGTGGTGGTGGATATGTT 59.995 52.381 0.00 0.00 0.00 2.71
1330 1383 0.106519 CATCCCCCTCATGGACAACC 60.107 60.000 0.00 0.00 33.94 3.77
1331 1384 0.625849 ACATCCCCCTCATGGACAAC 59.374 55.000 0.00 0.00 33.94 3.32
1332 1385 2.126882 CTACATCCCCCTCATGGACAA 58.873 52.381 0.00 0.00 33.94 3.18
1333 1386 1.695664 CCTACATCCCCCTCATGGACA 60.696 57.143 0.00 0.00 33.94 4.02
1334 1387 1.059913 CCTACATCCCCCTCATGGAC 58.940 60.000 0.00 0.00 33.94 4.02
1335 1388 0.768221 GCCTACATCCCCCTCATGGA 60.768 60.000 0.00 0.00 35.39 3.41
1336 1389 1.061905 TGCCTACATCCCCCTCATGG 61.062 60.000 0.00 0.00 0.00 3.66
1337 1390 0.399454 CTGCCTACATCCCCCTCATG 59.601 60.000 0.00 0.00 0.00 3.07
1338 1391 1.422161 GCTGCCTACATCCCCCTCAT 61.422 60.000 0.00 0.00 0.00 2.90
1339 1392 2.072487 GCTGCCTACATCCCCCTCA 61.072 63.158 0.00 0.00 0.00 3.86
1340 1393 2.823758 GGCTGCCTACATCCCCCTC 61.824 68.421 12.43 0.00 0.00 4.30
1341 1394 1.973346 TAGGCTGCCTACATCCCCCT 61.973 60.000 24.10 0.00 32.11 4.79
1342 1395 1.461461 TAGGCTGCCTACATCCCCC 60.461 63.158 24.10 0.00 32.11 5.40
1343 1396 1.484444 CCTAGGCTGCCTACATCCCC 61.484 65.000 24.10 0.00 32.11 4.81
1344 1397 1.484444 CCCTAGGCTGCCTACATCCC 61.484 65.000 24.10 0.00 32.11 3.85
1857 1922 4.168883 AGGGTTTCATATCTAGCCTACCC 58.831 47.826 0.00 0.00 43.42 3.69
1912 1977 0.320374 TTTGGGCGAGAGTGGTACTG 59.680 55.000 0.00 0.00 0.00 2.74
1917 1982 3.909662 CCATTTGGGCGAGAGTGG 58.090 61.111 0.00 0.00 0.00 4.00
1988 2053 1.279271 CCTGGGAAGTCCTCGTGAAAT 59.721 52.381 0.00 0.00 36.20 2.17
2061 2126 4.700700 AGCCAACGTAAAAACTAGTCAGT 58.299 39.130 0.00 0.00 36.19 3.41
2065 2130 2.477754 GCGAGCCAACGTAAAAACTAGT 59.522 45.455 0.00 0.00 35.59 2.57
2139 2204 2.457598 TCAACTCCGCCTATGTCTTCT 58.542 47.619 0.00 0.00 0.00 2.85
2146 2211 1.743772 GCACACATCAACTCCGCCTAT 60.744 52.381 0.00 0.00 0.00 2.57
2160 2225 3.243941 ACGGTCTTATTGTACAGCACACA 60.244 43.478 0.00 0.00 36.69 3.72
2166 2231 7.745022 TCGATTTTACGGTCTTATTGTACAG 57.255 36.000 0.00 0.00 0.00 2.74
2321 2386 4.572389 GCATGAAGTATCCACCTTACAGTG 59.428 45.833 0.00 0.00 37.51 3.66
2406 2472 3.214328 ACAACTTTGCCTCTAGTGGTTG 58.786 45.455 12.31 10.26 38.60 3.77
2420 2486 9.037737 CAACTCATCAATTTTCATGACAACTTT 57.962 29.630 0.00 0.00 0.00 2.66
2447 2513 8.160106 AGATCTTGACTGTTTGTTCCTCTTAAT 58.840 33.333 0.00 0.00 0.00 1.40
2477 2543 6.952773 AACCAATTACTGCAGTTTCTGTAA 57.047 33.333 27.06 12.52 35.73 2.41
2568 2634 5.640732 GAAAACATATTGTTGAGCGACCAT 58.359 37.500 0.00 0.00 40.14 3.55
2620 2686 8.201464 TCACTAACAACTTGTAAGACTTGATCA 58.799 33.333 0.00 0.00 0.00 2.92
2722 2789 3.914364 GGACACGTGAATCTTCAAAATGC 59.086 43.478 25.01 0.00 39.21 3.56
2993 3060 6.914665 AGATGAATGATAACAAAGGATGGGA 58.085 36.000 0.00 0.00 0.00 4.37
3105 3172 5.451103 GCAGAAATATTCCTCCTCAAAAGGC 60.451 44.000 0.00 0.00 43.02 4.35
4139 4219 3.960571 AGAAGTCAAATAGGCACATGCT 58.039 40.909 3.48 0.00 41.70 3.79
4159 4239 4.649674 TGGTACAGTTCCTATAGCCTGAAG 59.350 45.833 15.23 0.00 0.00 3.02
4395 4475 8.055181 AGAATGACTAAAGGCAAATATGAGGAA 58.945 33.333 0.00 0.00 0.00 3.36
4675 4755 6.826893 ATGCATTTATTTTGTAACATCGCC 57.173 33.333 0.00 0.00 0.00 5.54
4868 4949 5.912892 ACAAAACCTACCCAAAACAATCAG 58.087 37.500 0.00 0.00 0.00 2.90
4919 5000 4.927425 GTGACGGCTTCAAAATGTCTACTA 59.073 41.667 0.00 0.00 35.39 1.82
4981 5071 2.653115 GCCTTGCCAGGTGCTTTC 59.347 61.111 5.61 0.00 43.18 2.62
5059 5149 1.576421 GAGTTCCAACAAGCAGGCG 59.424 57.895 0.00 0.00 0.00 5.52
5176 5267 6.379703 TGAGGTGAGAAAACCAGAAAAATGAA 59.620 34.615 0.00 0.00 43.20 2.57
5177 5268 5.890985 TGAGGTGAGAAAACCAGAAAAATGA 59.109 36.000 0.00 0.00 43.20 2.57
5178 5269 6.147864 TGAGGTGAGAAAACCAGAAAAATG 57.852 37.500 0.00 0.00 43.20 2.32
5179 5270 6.983906 ATGAGGTGAGAAAACCAGAAAAAT 57.016 33.333 0.00 0.00 43.20 1.82
5180 5271 6.790232 AATGAGGTGAGAAAACCAGAAAAA 57.210 33.333 0.00 0.00 43.20 1.94
5181 5272 8.359642 CAATAATGAGGTGAGAAAACCAGAAAA 58.640 33.333 0.00 0.00 43.20 2.29
5182 5273 7.523709 GCAATAATGAGGTGAGAAAACCAGAAA 60.524 37.037 0.00 0.00 43.20 2.52
5183 5274 6.071952 GCAATAATGAGGTGAGAAAACCAGAA 60.072 38.462 0.00 0.00 43.20 3.02
5184 5275 5.415701 GCAATAATGAGGTGAGAAAACCAGA 59.584 40.000 0.00 0.00 43.20 3.86
5281 5383 1.933021 AGGTCGGTTCAGGTCATGTA 58.067 50.000 0.00 0.00 0.00 2.29
5335 5437 7.676683 ATTCTAGCTTAGGAAGTTGTATCCA 57.323 36.000 0.00 0.00 39.55 3.41
5459 5885 4.462834 AGGTTAAGCAATTAGTTTCCAGCC 59.537 41.667 7.52 0.00 0.00 4.85
5905 6415 7.649306 GGCATCTAATTCAAAATTTACATCGCT 59.351 33.333 0.00 0.00 0.00 4.93
6264 6806 6.413783 TTCCTGAACATTAGTCTGTGTGTA 57.586 37.500 0.00 0.00 0.00 2.90
6446 6989 6.204688 CCTGCCATTTTAAAAAGAAAGGGAAC 59.795 38.462 4.44 0.00 39.59 3.62
6451 6994 7.095481 GCTTCTCCTGCCATTTTAAAAAGAAAG 60.095 37.037 4.44 2.10 0.00 2.62
6531 7074 3.696051 TGCTACTTTTGATGCAATCCCTC 59.304 43.478 0.00 0.00 44.73 4.30
6539 7082 6.486248 TCGATGTTTATGCTACTTTTGATGC 58.514 36.000 0.00 0.00 0.00 3.91
6600 7143 7.443302 TCTCTCAAGAGGGAATCAAATACAT 57.557 36.000 7.17 0.00 42.30 2.29
6642 7186 6.493166 TGAAATCATCTCCCACCTTTTACAT 58.507 36.000 0.00 0.00 0.00 2.29
6662 7208 5.060427 TCCAAGTCTTCAGGGAAATGAAA 57.940 39.130 0.00 0.00 38.66 2.69
6684 7230 1.004745 GGCATAATGGGGATGACCGAT 59.995 52.381 0.00 0.00 39.67 4.18
6698 7248 6.095580 TCAAGTTGTTTGTACACTTGGCATAA 59.904 34.615 18.03 2.01 40.22 1.90
6783 7334 3.775261 ATTGAAACCTTGGCTTGCATT 57.225 38.095 0.00 0.00 0.00 3.56
6810 7361 6.128172 CGAAATATGATGTTATTGGAGAGCCC 60.128 42.308 0.00 0.00 0.00 5.19
6823 7374 4.707105 TGGCTGATGTCGAAATATGATGT 58.293 39.130 0.00 0.00 0.00 3.06
6833 7384 1.071542 TGAAACCTTGGCTGATGTCGA 59.928 47.619 0.00 0.00 0.00 4.20
6834 7385 1.522668 TGAAACCTTGGCTGATGTCG 58.477 50.000 0.00 0.00 0.00 4.35
6881 7432 2.814805 ATGGGAAGGATGTCCAAGTG 57.185 50.000 1.30 0.00 39.70 3.16
6906 7457 8.525316 TGCAATAGAACAATCATGAAATCAGTT 58.475 29.630 0.00 0.37 0.00 3.16
6912 7463 6.209192 ACTGGTGCAATAGAACAATCATGAAA 59.791 34.615 0.00 0.00 0.00 2.69
6960 7511 5.233050 CGATGGATAAAGACAGTGCTACTTG 59.767 44.000 0.00 0.00 0.00 3.16
6971 7522 3.492756 GCAGAAGAGCGATGGATAAAGAC 59.507 47.826 0.00 0.00 0.00 3.01
7012 7573 0.602638 TGCTGTGCGGGTAGAAACTG 60.603 55.000 0.00 0.00 0.00 3.16
7043 7609 6.464895 GATGAATTGATCTCATCTTCGGAC 57.535 41.667 13.53 0.00 43.88 4.79
7085 7651 7.771927 TCTTATATTAGTTTACGGAGGGAGG 57.228 40.000 0.00 0.00 0.00 4.30
7086 7652 9.640963 CATTCTTATATTAGTTTACGGAGGGAG 57.359 37.037 0.00 0.00 0.00 4.30
7088 7654 9.774413 AACATTCTTATATTAGTTTACGGAGGG 57.226 33.333 0.00 0.00 0.00 4.30
7137 7703 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
7138 7704 8.910944 TCCTCTGTAAACTAATATAAGAGCGTT 58.089 33.333 0.00 0.00 0.00 4.84
7139 7705 8.461249 TCCTCTGTAAACTAATATAAGAGCGT 57.539 34.615 0.00 0.00 0.00 5.07
7140 7706 9.400638 CTTCCTCTGTAAACTAATATAAGAGCG 57.599 37.037 0.00 0.00 0.00 5.03
7168 7734 9.775854 CACAAGGAGATCAAGTATCAATCTAAT 57.224 33.333 0.00 0.00 37.03 1.73
7169 7735 7.712639 GCACAAGGAGATCAAGTATCAATCTAA 59.287 37.037 0.00 0.00 37.03 2.10
7170 7736 7.212976 GCACAAGGAGATCAAGTATCAATCTA 58.787 38.462 0.00 0.00 37.03 1.98
7171 7737 6.054295 GCACAAGGAGATCAAGTATCAATCT 58.946 40.000 0.00 0.00 37.03 2.40
7172 7738 5.050499 CGCACAAGGAGATCAAGTATCAATC 60.050 44.000 0.00 0.00 37.03 2.67
7173 7739 4.813161 CGCACAAGGAGATCAAGTATCAAT 59.187 41.667 0.00 0.00 37.03 2.57
7174 7740 4.183865 CGCACAAGGAGATCAAGTATCAA 58.816 43.478 0.00 0.00 37.03 2.57
7175 7741 3.785486 CGCACAAGGAGATCAAGTATCA 58.215 45.455 0.00 0.00 37.03 2.15
7176 7742 2.541762 GCGCACAAGGAGATCAAGTATC 59.458 50.000 0.30 0.00 34.52 2.24
7191 7757 2.158559 ACAGGAACAAATATGCGCACA 58.841 42.857 14.90 0.00 0.00 4.57
7264 7831 4.390129 GTCTAGAGATATCCTGGACCCA 57.610 50.000 18.64 0.00 36.51 4.51
7271 7838 4.708576 TGACGTGGTCTAGAGATATCCT 57.291 45.455 0.00 0.00 33.15 3.24
7311 7878 3.243704 GCAGGATTATCTCGAGCTCAAGT 60.244 47.826 15.40 0.00 0.00 3.16
7335 7902 3.479505 TTGTGTTGTTTTGTGAGTCGG 57.520 42.857 0.00 0.00 0.00 4.79
7342 7909 2.440539 TGCGGTTTGTGTTGTTTTGT 57.559 40.000 0.00 0.00 0.00 2.83
7344 7911 2.275318 CCATGCGGTTTGTGTTGTTTT 58.725 42.857 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.