Multiple sequence alignment - TraesCS2D01G264500

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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 TraesCS2D01G264500 chr2D 100.000 2710 0 0 1 2710 323560371 323563080 0.000000e+00 5005.0
1 TraesCS2D01G264500 chr2D 89.768 733 63 7 996 1721 323517061 323516334 0.000000e+00 928.0
2 TraesCS2D01G264500 chr2D 95.935 123 5 0 2016 2138 437797618 437797740 1.650000e-47 200.0
3 TraesCS2D01G264500 chr2D 100.000 50 0 0 1 50 323551750 323551799 2.870000e-15 93.5
4 TraesCS2D01G264500 chr2A 95.649 1287 43 10 585 1866 406964708 406963430 0.000000e+00 2054.0
5 TraesCS2D01G264500 chr2A 95.649 1287 42 10 585 1866 407092883 407091606 0.000000e+00 2054.0
6 TraesCS2D01G264500 chr2A 89.024 738 67 11 985 1711 406996926 406997660 0.000000e+00 902.0
7 TraesCS2D01G264500 chr2A 88.889 738 68 11 985 1711 407125423 407126157 0.000000e+00 896.0
8 TraesCS2D01G264500 chr2A 84.053 533 62 14 52 574 407093449 407092930 2.420000e-135 492.0
9 TraesCS2D01G264500 chr2A 83.677 533 64 14 52 574 406965274 406964755 5.250000e-132 481.0
10 TraesCS2D01G264500 chr2B 94.421 1183 50 9 695 1873 391523022 391524192 0.000000e+00 1805.0
11 TraesCS2D01G264500 chr2B 88.936 714 71 6 996 1707 111669408 111668701 0.000000e+00 874.0
12 TraesCS2D01G264500 chr2B 89.983 589 37 9 2139 2707 560272327 560272913 0.000000e+00 741.0
13 TraesCS2D01G264500 chr2B 90.909 132 12 0 1888 2019 560272208 560272339 7.710000e-41 178.0
14 TraesCS2D01G264500 chr2B 100.000 51 0 0 1 51 470324288 470324238 7.990000e-16 95.3
15 TraesCS2D01G264500 chr4D 91.787 621 50 1 1107 1726 354036797 354037417 0.000000e+00 863.0
16 TraesCS2D01G264500 chr4D 86.603 418 28 10 2139 2528 381561029 381561446 1.150000e-118 436.0
17 TraesCS2D01G264500 chr4D 88.649 185 21 0 2523 2707 381562377 381562561 2.710000e-55 226.0
18 TraesCS2D01G264500 chr4D 91.406 128 10 1 1889 2015 381560910 381561037 9.970000e-40 174.0
19 TraesCS2D01G264500 chr4B 91.489 611 52 0 1116 1726 437747897 437748507 0.000000e+00 841.0
20 TraesCS2D01G264500 chr4A 89.358 592 41 6 2139 2710 719850258 719849669 0.000000e+00 725.0
21 TraesCS2D01G264500 chr4A 90.977 133 11 1 1888 2019 719850378 719850246 7.710000e-41 178.0
22 TraesCS2D01G264500 chr4A 94.545 55 2 1 1 55 268293927 268293980 1.730000e-12 84.2
23 TraesCS2D01G264500 chr7A 87.231 603 39 14 2139 2705 111150308 111150908 0.000000e+00 652.0
24 TraesCS2D01G264500 chr7A 86.379 602 43 15 2139 2705 111113869 111114466 2.960000e-174 621.0
25 TraesCS2D01G264500 chr7A 95.935 123 5 0 2016 2138 392610699 392610577 1.650000e-47 200.0
26 TraesCS2D01G264500 chr5B 91.589 321 25 2 2386 2705 566124989 566124670 2.480000e-120 442.0
27 TraesCS2D01G264500 chr5B 83.273 275 25 7 2139 2392 566130737 566130463 1.620000e-57 233.0
28 TraesCS2D01G264500 chr5B 91.473 129 10 1 1888 2015 566130857 566130729 2.770000e-40 176.0
29 TraesCS2D01G264500 chr6A 81.055 417 70 5 100 515 15880990 15880582 9.360000e-85 324.0
30 TraesCS2D01G264500 chr6D 79.714 350 55 5 118 467 14728808 14728475 3.490000e-59 239.0
31 TraesCS2D01G264500 chr6D 95.122 123 6 0 2016 2138 345490425 345490303 7.660000e-46 195.0
32 TraesCS2D01G264500 chr3A 95.385 130 6 0 2010 2139 599708001 599708130 9.830000e-50 207.0
33 TraesCS2D01G264500 chr3D 91.781 146 8 4 2008 2152 540108390 540108248 1.650000e-47 200.0
34 TraesCS2D01G264500 chr3D 86.861 137 16 2 2380 2515 54332251 54332116 4.670000e-33 152.0
35 TraesCS2D01G264500 chr3D 98.039 51 1 0 1 51 256872279 256872329 3.720000e-14 89.8
36 TraesCS2D01G264500 chr1D 95.935 123 5 0 2016 2138 315879128 315879250 1.650000e-47 200.0
37 TraesCS2D01G264500 chr5D 93.130 131 9 0 2009 2139 31817425 31817555 2.750000e-45 193.0
38 TraesCS2D01G264500 chr3B 93.750 128 8 0 2011 2138 541059928 541059801 2.750000e-45 193.0
39 TraesCS2D01G264500 chr7D 93.077 130 9 0 2016 2145 445779706 445779577 9.900000e-45 191.0
40 TraesCS2D01G264500 chr7D 75.443 395 80 9 98 483 99183911 99184297 2.770000e-40 176.0
41 TraesCS2D01G264500 chr7D 87.591 137 15 2 2380 2515 40672591 40672456 1.000000e-34 158.0
42 TraesCS2D01G264500 chr7D 100.000 50 0 0 1 50 482265490 482265539 2.870000e-15 93.5
43 TraesCS2D01G264500 chr7D 98.039 51 1 0 1 51 73842743 73842693 3.720000e-14 89.8
44 TraesCS2D01G264500 chr6B 98.000 50 1 0 2 51 98491783 98491832 1.340000e-13 87.9
45 TraesCS2D01G264500 chr6B 98.000 50 1 0 2 51 98578507 98578556 1.340000e-13 87.9
46 TraesCS2D01G264500 chr6B 98.000 50 1 0 2 51 98643252 98643301 1.340000e-13 87.9


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 TraesCS2D01G264500 chr2D 323560371 323563080 2709 False 5005.000000 5005 100.0000 1 2710 1 chr2D.!!$F2 2709
1 TraesCS2D01G264500 chr2D 323516334 323517061 727 True 928.000000 928 89.7680 996 1721 1 chr2D.!!$R1 725
2 TraesCS2D01G264500 chr2A 407091606 407093449 1843 True 1273.000000 2054 89.8510 52 1866 2 chr2A.!!$R2 1814
3 TraesCS2D01G264500 chr2A 406963430 406965274 1844 True 1267.500000 2054 89.6630 52 1866 2 chr2A.!!$R1 1814
4 TraesCS2D01G264500 chr2A 406996926 406997660 734 False 902.000000 902 89.0240 985 1711 1 chr2A.!!$F1 726
5 TraesCS2D01G264500 chr2A 407125423 407126157 734 False 896.000000 896 88.8890 985 1711 1 chr2A.!!$F2 726
6 TraesCS2D01G264500 chr2B 391523022 391524192 1170 False 1805.000000 1805 94.4210 695 1873 1 chr2B.!!$F1 1178
7 TraesCS2D01G264500 chr2B 111668701 111669408 707 True 874.000000 874 88.9360 996 1707 1 chr2B.!!$R1 711
8 TraesCS2D01G264500 chr2B 560272208 560272913 705 False 459.500000 741 90.4460 1888 2707 2 chr2B.!!$F2 819
9 TraesCS2D01G264500 chr4D 354036797 354037417 620 False 863.000000 863 91.7870 1107 1726 1 chr4D.!!$F1 619
10 TraesCS2D01G264500 chr4D 381560910 381562561 1651 False 278.666667 436 88.8860 1889 2707 3 chr4D.!!$F2 818
11 TraesCS2D01G264500 chr4B 437747897 437748507 610 False 841.000000 841 91.4890 1116 1726 1 chr4B.!!$F1 610
12 TraesCS2D01G264500 chr4A 719849669 719850378 709 True 451.500000 725 90.1675 1888 2710 2 chr4A.!!$R1 822
13 TraesCS2D01G264500 chr7A 111150308 111150908 600 False 652.000000 652 87.2310 2139 2705 1 chr7A.!!$F2 566
14 TraesCS2D01G264500 chr7A 111113869 111114466 597 False 621.000000 621 86.3790 2139 2705 1 chr7A.!!$F1 566

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
331 335 0.036577 CTCAGGTGGCTGAGTTCTGG 60.037 60.0 0.0 0.0 44.16 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 2151 0.03759 GGTCACTAACATGTGGGCCA 59.962 55.0 0.0 0.0 38.4 5.36 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
26 27 9.793252 CAACTAAAATAAATGGAAGACATCTGG 57.207 33.333 0.00 0.00 39.40 3.86
27 28 9.753674 AACTAAAATAAATGGAAGACATCTGGA 57.246 29.630 0.00 0.00 39.40 3.86
28 29 9.401058 ACTAAAATAAATGGAAGACATCTGGAG 57.599 33.333 0.00 0.00 39.40 3.86
29 30 6.705863 AAATAAATGGAAGACATCTGGAGC 57.294 37.500 0.00 0.00 39.40 4.70
30 31 3.726557 AAATGGAAGACATCTGGAGCA 57.273 42.857 0.00 0.00 39.40 4.26
31 32 3.947612 AATGGAAGACATCTGGAGCAT 57.052 42.857 0.00 0.00 39.40 3.79
32 33 2.996249 TGGAAGACATCTGGAGCATC 57.004 50.000 0.00 0.00 0.00 3.91
33 34 1.137675 TGGAAGACATCTGGAGCATCG 59.862 52.381 0.00 0.00 34.37 3.84
34 35 1.539929 GGAAGACATCTGGAGCATCGG 60.540 57.143 0.00 0.00 34.37 4.18
35 36 1.137872 GAAGACATCTGGAGCATCGGT 59.862 52.381 0.00 0.00 34.37 4.69
36 37 0.749649 AGACATCTGGAGCATCGGTC 59.250 55.000 0.00 0.00 34.37 4.79
37 38 0.749649 GACATCTGGAGCATCGGTCT 59.250 55.000 0.00 0.00 34.37 3.85
38 39 0.749649 ACATCTGGAGCATCGGTCTC 59.250 55.000 0.00 0.00 34.37 3.36
39 40 0.318529 CATCTGGAGCATCGGTCTCG 60.319 60.000 0.00 0.00 34.37 4.04
40 41 1.459455 ATCTGGAGCATCGGTCTCGG 61.459 60.000 0.00 0.00 34.37 4.63
41 42 3.144120 CTGGAGCATCGGTCTCGGG 62.144 68.421 0.00 0.00 34.37 5.14
42 43 3.917760 GGAGCATCGGTCTCGGGG 61.918 72.222 0.00 0.00 34.37 5.73
43 44 4.593864 GAGCATCGGTCTCGGGGC 62.594 72.222 0.00 0.00 36.95 5.80
46 47 4.143333 CATCGGTCTCGGGGCGTT 62.143 66.667 0.00 0.00 36.95 4.84
47 48 2.440796 ATCGGTCTCGGGGCGTTA 60.441 61.111 0.00 0.00 36.95 3.18
48 49 2.779033 ATCGGTCTCGGGGCGTTAC 61.779 63.158 0.00 0.00 36.95 2.50
49 50 3.751246 CGGTCTCGGGGCGTTACA 61.751 66.667 0.00 0.00 0.00 2.41
50 51 2.125793 GGTCTCGGGGCGTTACAC 60.126 66.667 0.00 0.00 0.00 2.90
65 66 3.120889 CGTTACACGTCGAGACTTCTGTA 60.121 47.826 0.00 0.00 36.74 2.74
70 71 2.243407 CGTCGAGACTTCTGTAGCAAC 58.757 52.381 1.56 0.00 0.00 4.17
71 72 2.350484 CGTCGAGACTTCTGTAGCAACA 60.350 50.000 1.56 0.00 0.00 3.33
88 89 2.134789 ACAATGATGAGGGGAGCAAC 57.865 50.000 0.00 0.00 0.00 4.17
90 91 0.911769 AATGATGAGGGGAGCAACGA 59.088 50.000 0.00 0.00 0.00 3.85
92 93 1.191489 TGATGAGGGGAGCAACGACA 61.191 55.000 0.00 0.00 0.00 4.35
93 94 0.460987 GATGAGGGGAGCAACGACAG 60.461 60.000 0.00 0.00 0.00 3.51
96 97 1.534235 AGGGGAGCAACGACAGAGT 60.534 57.895 0.00 0.00 0.00 3.24
100 102 0.946221 GGAGCAACGACAGAGTGTGG 60.946 60.000 0.00 0.00 32.08 4.17
102 104 1.887242 GCAACGACAGAGTGTGGCA 60.887 57.895 0.00 0.00 30.77 4.92
116 118 1.702401 TGTGGCAATGGTTGAGGTAGA 59.298 47.619 0.00 0.00 0.00 2.59
119 121 1.369625 GCAATGGTTGAGGTAGACGG 58.630 55.000 0.00 0.00 0.00 4.79
127 129 1.752683 TGAGGTAGACGGCTCTTCTC 58.247 55.000 0.00 0.41 0.00 2.87
136 138 2.507324 GCTCTTCTCCGGCGTGTC 60.507 66.667 6.01 0.00 0.00 3.67
137 139 2.995872 GCTCTTCTCCGGCGTGTCT 61.996 63.158 6.01 0.00 0.00 3.41
160 162 1.508088 GATTGCCTCGCCTGGTTTG 59.492 57.895 0.00 0.00 0.00 2.93
166 168 1.600023 CCTCGCCTGGTTTGTTGTTA 58.400 50.000 0.00 0.00 0.00 2.41
170 172 1.331138 CGCCTGGTTTGTTGTTACGAA 59.669 47.619 0.00 0.00 0.00 3.85
181 185 1.415374 TGTTACGAAGTCGAAGCTGC 58.585 50.000 7.87 0.00 43.93 5.25
182 186 0.362512 GTTACGAAGTCGAAGCTGCG 59.637 55.000 8.15 8.15 43.93 5.18
217 221 1.956170 GGCATACGATGACGGGCAG 60.956 63.158 0.00 0.00 44.46 4.85
252 256 3.496131 GATCTTTCGCGGCGCCAA 61.496 61.111 28.98 18.55 0.00 4.52
280 284 4.873259 GCCTACTTCTCCTTTGTGATTCTC 59.127 45.833 0.00 0.00 0.00 2.87
281 285 5.337975 GCCTACTTCTCCTTTGTGATTCTCT 60.338 44.000 0.00 0.00 0.00 3.10
297 301 1.555533 TCTCTGTCAGAGTCGGAGCTA 59.444 52.381 25.68 4.83 42.83 3.32
298 302 2.171659 TCTCTGTCAGAGTCGGAGCTAT 59.828 50.000 25.68 0.00 42.83 2.97
300 304 2.020720 CTGTCAGAGTCGGAGCTATGT 58.979 52.381 0.00 0.00 0.00 2.29
302 306 2.164422 TGTCAGAGTCGGAGCTATGTTG 59.836 50.000 0.00 0.00 0.00 3.33
303 307 2.164624 GTCAGAGTCGGAGCTATGTTGT 59.835 50.000 0.00 0.00 0.00 3.32
304 308 2.423892 TCAGAGTCGGAGCTATGTTGTC 59.576 50.000 0.00 0.00 0.00 3.18
305 309 2.425312 CAGAGTCGGAGCTATGTTGTCT 59.575 50.000 0.00 0.00 0.00 3.41
306 310 2.425312 AGAGTCGGAGCTATGTTGTCTG 59.575 50.000 0.00 0.00 0.00 3.51
307 311 1.478510 AGTCGGAGCTATGTTGTCTGG 59.521 52.381 0.00 0.00 0.00 3.86
308 312 1.204941 GTCGGAGCTATGTTGTCTGGT 59.795 52.381 0.00 0.00 0.00 4.00
309 313 1.476891 TCGGAGCTATGTTGTCTGGTC 59.523 52.381 0.00 0.00 0.00 4.02
310 314 1.799181 CGGAGCTATGTTGTCTGGTCG 60.799 57.143 0.00 0.00 0.00 4.79
311 315 1.204941 GGAGCTATGTTGTCTGGTCGT 59.795 52.381 0.00 0.00 0.00 4.34
312 316 2.531206 GAGCTATGTTGTCTGGTCGTC 58.469 52.381 0.00 0.00 0.00 4.20
313 317 2.164624 GAGCTATGTTGTCTGGTCGTCT 59.835 50.000 0.00 0.00 0.00 4.18
314 318 2.164624 AGCTATGTTGTCTGGTCGTCTC 59.835 50.000 0.00 0.00 0.00 3.36
331 335 0.036577 CTCAGGTGGCTGAGTTCTGG 60.037 60.000 0.00 0.00 44.16 3.86
332 336 0.764369 TCAGGTGGCTGAGTTCTGGT 60.764 55.000 0.00 0.00 0.00 4.00
342 346 1.347707 TGAGTTCTGGTGCGGATCTTT 59.652 47.619 0.00 0.00 0.00 2.52
346 350 5.070446 TGAGTTCTGGTGCGGATCTTTATAT 59.930 40.000 0.00 0.00 0.00 0.86
352 356 6.892456 TCTGGTGCGGATCTTTATATATCTCT 59.108 38.462 0.00 0.00 0.00 3.10
373 377 2.764269 ACATGGCCTCTATAGTGTGGT 58.236 47.619 3.32 0.00 0.00 4.16
380 384 3.681874 GCCTCTATAGTGTGGTTTGGGTC 60.682 52.174 0.00 0.00 0.00 4.46
383 387 4.028131 TCTATAGTGTGGTTTGGGTCGAT 58.972 43.478 0.00 0.00 0.00 3.59
414 418 0.935196 GCAAAGTCGGAGTCGTTTGT 59.065 50.000 0.00 0.00 35.87 2.83
417 421 1.484356 AAGTCGGAGTCGTTTGTTCG 58.516 50.000 0.00 0.00 37.69 3.95
430 434 3.124636 CGTTTGTTCGGAGTTTAGGGATG 59.875 47.826 0.00 0.00 0.00 3.51
436 440 3.028850 TCGGAGTTTAGGGATGACGATT 58.971 45.455 0.00 0.00 0.00 3.34
439 443 4.923871 CGGAGTTTAGGGATGACGATTATG 59.076 45.833 0.00 0.00 0.00 1.90
440 444 5.278808 CGGAGTTTAGGGATGACGATTATGA 60.279 44.000 0.00 0.00 0.00 2.15
441 445 6.522054 GGAGTTTAGGGATGACGATTATGAA 58.478 40.000 0.00 0.00 0.00 2.57
443 447 7.661847 GGAGTTTAGGGATGACGATTATGAATT 59.338 37.037 0.00 0.00 0.00 2.17
462 466 4.993705 ATTTAGGGAAGAAGTGGTGACA 57.006 40.909 0.00 0.00 38.70 3.58
463 467 4.781775 TTTAGGGAAGAAGTGGTGACAA 57.218 40.909 0.00 0.00 46.06 3.18
470 474 4.154918 GGAAGAAGTGGTGACAATGACATC 59.845 45.833 0.00 0.00 46.06 3.06
483 487 4.883585 ACAATGACATCTGTGTGTTGTCTT 59.116 37.500 4.19 0.00 42.71 3.01
484 488 5.008019 ACAATGACATCTGTGTGTTGTCTTC 59.992 40.000 4.19 0.00 42.71 2.87
490 494 0.101579 TGTGTGTTGTCTTCGCGAGA 59.898 50.000 9.59 6.53 39.20 4.04
524 528 2.769663 TGGTCTGTGCGGGATAACTTAT 59.230 45.455 0.00 0.00 0.00 1.73
529 533 4.403113 TCTGTGCGGGATAACTTATGTGTA 59.597 41.667 0.00 0.00 0.00 2.90
534 539 4.365723 CGGGATAACTTATGTGTACGCTT 58.634 43.478 8.10 3.93 0.00 4.68
538 543 5.981315 GGATAACTTATGTGTACGCTTAGCA 59.019 40.000 8.10 0.00 0.00 3.49
555 560 6.249260 CGCTTAGCAGTTGTGATGATTTTTAC 59.751 38.462 4.70 0.00 0.00 2.01
559 570 7.054491 AGCAGTTGTGATGATTTTTACCTTT 57.946 32.000 0.00 0.00 0.00 3.11
578 621 4.215613 CCTTTATAATTAACCGGGCTGAGC 59.784 45.833 6.32 0.00 0.00 4.26
584 627 0.248289 TAACCGGGCTGAGCAACTAC 59.752 55.000 6.82 0.00 0.00 2.73
587 630 0.741221 CCGGGCTGAGCAACTACTTC 60.741 60.000 6.82 0.00 0.00 3.01
588 631 0.247736 CGGGCTGAGCAACTACTTCT 59.752 55.000 6.82 0.00 0.00 2.85
592 642 4.518249 GGGCTGAGCAACTACTTCTTAAT 58.482 43.478 6.82 0.00 0.00 1.40
593 643 5.671493 GGGCTGAGCAACTACTTCTTAATA 58.329 41.667 6.82 0.00 0.00 0.98
597 647 6.019156 GCTGAGCAACTACTTCTTAATAGCAG 60.019 42.308 0.00 0.00 0.00 4.24
606 656 9.608718 ACTACTTCTTAATAGCAGGAATCCTAT 57.391 33.333 0.00 0.00 29.64 2.57
613 663 9.956640 CTTAATAGCAGGAATCCTATCATTTCT 57.043 33.333 0.00 0.00 29.64 2.52
614 664 9.950496 TTAATAGCAGGAATCCTATCATTTCTC 57.050 33.333 0.00 0.00 29.64 2.87
615 665 4.892433 AGCAGGAATCCTATCATTTCTCG 58.108 43.478 0.00 0.00 29.64 4.04
618 668 5.178438 GCAGGAATCCTATCATTTCTCGAAC 59.822 44.000 0.00 0.00 29.64 3.95
623 673 8.458843 GGAATCCTATCATTTCTCGAACAAAAA 58.541 33.333 0.00 0.00 0.00 1.94
819 869 6.051717 GTCGTACCTGGATAAGACAGTACTA 58.948 44.000 0.00 0.00 34.73 1.82
849 899 2.551459 CAGCCTCACTTTCCAGAAACTG 59.449 50.000 0.00 0.00 0.00 3.16
853 903 4.061596 CCTCACTTTCCAGAAACTGAGAC 58.938 47.826 21.55 0.00 40.50 3.36
893 948 3.752665 TCTATAAGTACCGGAGCCTCTG 58.247 50.000 9.46 0.00 0.00 3.35
913 968 6.098982 CCTCTGTATATTCTTCCTTCACCACT 59.901 42.308 0.00 0.00 0.00 4.00
1028 1083 6.924060 GCCACTAAGATCTACATCGTGTAATT 59.076 38.462 0.00 0.00 31.67 1.40
1039 1094 1.822990 TCGTGTAATTCTCCGCCTCTT 59.177 47.619 0.00 0.00 0.00 2.85
1086 1148 2.349249 CGAGCTGAATGATTTGATCGCC 60.349 50.000 0.00 0.00 0.00 5.54
1087 1149 2.877168 GAGCTGAATGATTTGATCGCCT 59.123 45.455 0.00 0.00 0.00 5.52
1179 1248 3.391665 ATGAAGAAGGGCGCCGAGG 62.392 63.158 22.54 0.00 0.00 4.63
1257 1326 1.675310 CTGGGGAAGATGCACGCAA 60.675 57.895 0.00 0.00 0.00 4.85
1794 1863 7.111593 CAGTCGTGAAACAATTTAAGCTGTAAC 59.888 37.037 0.00 0.00 35.74 2.50
1849 1918 4.177026 ACGAGAATCTATTCTGTGTGCAC 58.823 43.478 10.75 10.75 46.47 4.57
1855 1924 2.371841 TCTATTCTGTGTGCACCCACTT 59.628 45.455 15.69 0.00 42.54 3.16
1974 2044 0.107993 CGAGATGTGTGATGGCCTGT 60.108 55.000 3.32 0.00 0.00 4.00
1976 2046 2.440409 GAGATGTGTGATGGCCTGTTT 58.560 47.619 3.32 0.00 0.00 2.83
2000 2070 5.121105 GGGTTAACCATCGTTATTAGCAGT 58.879 41.667 25.71 0.00 39.85 4.40
2004 2074 8.833493 GGTTAACCATCGTTATTAGCAGTATTT 58.167 33.333 20.12 0.00 34.44 1.40
2007 2077 7.653767 ACCATCGTTATTAGCAGTATTTAGC 57.346 36.000 0.00 0.00 0.00 3.09
2008 2078 6.365247 ACCATCGTTATTAGCAGTATTTAGCG 59.635 38.462 0.00 0.00 35.48 4.26
2009 2079 5.817616 TCGTTATTAGCAGTATTTAGCGC 57.182 39.130 0.00 0.00 35.48 5.92
2010 2080 5.283294 TCGTTATTAGCAGTATTTAGCGCA 58.717 37.500 11.47 0.00 35.48 6.09
2011 2081 5.749588 TCGTTATTAGCAGTATTTAGCGCAA 59.250 36.000 11.47 0.00 35.48 4.85
2012 2082 6.065153 CGTTATTAGCAGTATTTAGCGCAAG 58.935 40.000 11.47 0.00 35.48 4.01
2013 2083 6.074516 CGTTATTAGCAGTATTTAGCGCAAGA 60.075 38.462 11.47 0.00 43.02 3.02
2014 2084 5.914085 ATTAGCAGTATTTAGCGCAAGAG 57.086 39.130 11.47 0.00 43.02 2.85
2015 2085 2.555199 AGCAGTATTTAGCGCAAGAGG 58.445 47.619 11.47 0.00 43.02 3.69
2016 2086 1.599542 GCAGTATTTAGCGCAAGAGGG 59.400 52.381 11.47 0.00 43.02 4.30
2017 2087 2.741878 GCAGTATTTAGCGCAAGAGGGA 60.742 50.000 11.47 0.00 43.02 4.20
2018 2088 2.866762 CAGTATTTAGCGCAAGAGGGAC 59.133 50.000 11.47 0.00 43.02 4.46
2020 2090 3.958798 AGTATTTAGCGCAAGAGGGACTA 59.041 43.478 11.47 0.00 41.55 2.59
2021 2091 4.589374 AGTATTTAGCGCAAGAGGGACTAT 59.411 41.667 11.47 0.00 41.55 2.12
2022 2092 5.773680 AGTATTTAGCGCAAGAGGGACTATA 59.226 40.000 11.47 0.00 41.55 1.31
2023 2093 4.317671 TTTAGCGCAAGAGGGACTATAC 57.682 45.455 11.47 0.00 41.55 1.47
2024 2094 2.074729 AGCGCAAGAGGGACTATACT 57.925 50.000 11.47 0.00 41.55 2.12
2025 2095 2.389715 AGCGCAAGAGGGACTATACTT 58.610 47.619 11.47 0.00 41.55 2.24
2026 2096 2.362717 AGCGCAAGAGGGACTATACTTC 59.637 50.000 11.47 0.00 41.55 3.01
2027 2097 2.859032 GCGCAAGAGGGACTATACTTCG 60.859 54.545 0.30 0.00 41.55 3.79
2028 2098 2.287668 CGCAAGAGGGACTATACTTCGG 60.288 54.545 0.00 0.00 41.55 4.30
2029 2099 2.694109 GCAAGAGGGACTATACTTCGGT 59.306 50.000 0.00 0.00 41.55 4.69
2030 2100 3.491104 GCAAGAGGGACTATACTTCGGTG 60.491 52.174 0.00 0.00 41.55 4.94
2031 2101 2.308690 AGAGGGACTATACTTCGGTGC 58.691 52.381 0.00 0.00 41.55 5.01
2032 2102 1.340568 GAGGGACTATACTTCGGTGCC 59.659 57.143 0.00 0.00 41.55 5.01
2033 2103 1.063114 AGGGACTATACTTCGGTGCCT 60.063 52.381 0.00 0.00 44.78 4.75
2034 2104 1.761198 GGGACTATACTTCGGTGCCTT 59.239 52.381 0.00 0.00 38.22 4.35
2035 2105 2.961062 GGGACTATACTTCGGTGCCTTA 59.039 50.000 0.00 0.00 38.22 2.69
2036 2106 3.385755 GGGACTATACTTCGGTGCCTTAA 59.614 47.826 0.00 0.00 38.22 1.85
2037 2107 4.501058 GGGACTATACTTCGGTGCCTTAAG 60.501 50.000 0.00 0.00 38.22 1.85
2038 2108 4.501058 GGACTATACTTCGGTGCCTTAAGG 60.501 50.000 17.81 17.81 38.53 2.69
2051 2121 2.876581 CCTTAAGGCACCTTCCTTTGT 58.123 47.619 9.00 0.00 43.62 2.83
2052 2122 2.558359 CCTTAAGGCACCTTCCTTTGTG 59.442 50.000 9.00 0.00 43.62 3.33
2053 2123 3.222603 CTTAAGGCACCTTCCTTTGTGT 58.777 45.455 4.91 0.00 43.62 3.72
2054 2124 1.692411 AAGGCACCTTCCTTTGTGTC 58.308 50.000 0.00 0.00 43.62 3.67
2055 2125 0.846693 AGGCACCTTCCTTTGTGTCT 59.153 50.000 0.00 0.00 42.30 3.41
2056 2126 2.054799 AGGCACCTTCCTTTGTGTCTA 58.945 47.619 0.00 0.00 45.05 2.59
2057 2127 2.644798 AGGCACCTTCCTTTGTGTCTAT 59.355 45.455 0.00 0.00 45.05 1.98
2058 2128 2.749621 GGCACCTTCCTTTGTGTCTATG 59.250 50.000 0.00 0.00 34.34 2.23
2059 2129 3.559171 GGCACCTTCCTTTGTGTCTATGA 60.559 47.826 0.00 0.00 34.34 2.15
2060 2130 3.437049 GCACCTTCCTTTGTGTCTATGAC 59.563 47.826 0.00 0.00 34.94 3.06
2061 2131 4.641396 CACCTTCCTTTGTGTCTATGACA 58.359 43.478 0.00 0.00 40.50 3.58
2062 2132 5.248640 CACCTTCCTTTGTGTCTATGACAT 58.751 41.667 3.65 0.00 44.63 3.06
2063 2133 5.122869 CACCTTCCTTTGTGTCTATGACATG 59.877 44.000 3.65 0.00 44.63 3.21
2064 2134 5.221925 ACCTTCCTTTGTGTCTATGACATGT 60.222 40.000 0.00 0.00 44.63 3.21
2065 2135 5.122869 CCTTCCTTTGTGTCTATGACATGTG 59.877 44.000 1.15 0.00 44.63 3.21
2066 2136 4.578871 TCCTTTGTGTCTATGACATGTGG 58.421 43.478 1.15 0.00 44.63 4.17
2067 2137 3.691118 CCTTTGTGTCTATGACATGTGGG 59.309 47.826 1.15 2.15 44.63 4.61
2068 2138 2.401583 TGTGTCTATGACATGTGGGC 57.598 50.000 1.15 0.00 44.63 5.36
2069 2139 1.065491 TGTGTCTATGACATGTGGGCC 60.065 52.381 1.15 0.00 44.63 5.80
2070 2140 0.546122 TGTCTATGACATGTGGGCCC 59.454 55.000 17.59 17.59 37.67 5.80
2071 2141 0.546122 GTCTATGACATGTGGGCCCA 59.454 55.000 24.45 24.45 32.09 5.36
2072 2142 1.064758 GTCTATGACATGTGGGCCCAA 60.065 52.381 30.64 17.87 32.09 4.12
2073 2143 1.064758 TCTATGACATGTGGGCCCAAC 60.065 52.381 30.64 21.29 0.00 3.77
2074 2144 0.701147 TATGACATGTGGGCCCAACA 59.299 50.000 30.64 26.33 0.00 3.33
2075 2145 0.612732 ATGACATGTGGGCCCAACAG 60.613 55.000 30.64 21.28 0.00 3.16
2076 2146 1.978617 GACATGTGGGCCCAACAGG 60.979 63.158 30.64 28.19 39.47 4.00
2077 2147 2.118076 CATGTGGGCCCAACAGGT 59.882 61.111 30.64 10.25 38.26 4.00
2078 2148 2.118076 ATGTGGGCCCAACAGGTG 59.882 61.111 30.64 0.00 38.26 4.00
2087 2157 4.601794 CAACAGGTGGCTGGCCCA 62.602 66.667 9.28 0.00 42.79 5.36
2094 2164 3.175304 TGGCTGGCCCACATGTTA 58.825 55.556 9.28 0.00 39.18 2.41
2095 2165 1.001020 TGGCTGGCCCACATGTTAG 60.001 57.895 9.28 0.00 39.18 2.34
2096 2166 1.000896 GGCTGGCCCACATGTTAGT 60.001 57.895 0.00 0.00 0.00 2.24
2097 2167 1.315257 GGCTGGCCCACATGTTAGTG 61.315 60.000 0.00 0.00 39.21 2.74
2098 2168 0.322456 GCTGGCCCACATGTTAGTGA 60.322 55.000 0.00 0.00 42.05 3.41
2099 2169 1.453155 CTGGCCCACATGTTAGTGAC 58.547 55.000 0.00 0.00 42.05 3.67
2100 2170 0.037590 TGGCCCACATGTTAGTGACC 59.962 55.000 0.00 0.00 42.05 4.02
2101 2171 0.037590 GGCCCACATGTTAGTGACCA 59.962 55.000 0.00 0.00 42.05 4.02
2102 2172 1.546773 GGCCCACATGTTAGTGACCAA 60.547 52.381 0.00 0.00 42.05 3.67
2103 2173 2.235016 GCCCACATGTTAGTGACCAAA 58.765 47.619 0.00 0.00 42.05 3.28
2104 2174 2.625790 GCCCACATGTTAGTGACCAAAA 59.374 45.455 0.00 0.00 42.05 2.44
2105 2175 3.305335 GCCCACATGTTAGTGACCAAAAG 60.305 47.826 0.00 0.00 42.05 2.27
2106 2176 3.255642 CCCACATGTTAGTGACCAAAAGG 59.744 47.826 0.00 0.00 42.05 3.11
2107 2177 3.305335 CCACATGTTAGTGACCAAAAGGC 60.305 47.826 0.00 0.00 42.05 4.35
2108 2178 3.317711 CACATGTTAGTGACCAAAAGGCA 59.682 43.478 0.00 0.00 42.05 4.75
2109 2179 3.569701 ACATGTTAGTGACCAAAAGGCAG 59.430 43.478 0.00 0.00 0.00 4.85
2110 2180 2.582052 TGTTAGTGACCAAAAGGCAGG 58.418 47.619 0.00 0.00 0.00 4.85
2111 2181 2.092103 TGTTAGTGACCAAAAGGCAGGT 60.092 45.455 0.00 0.00 41.83 4.00
2112 2182 2.270352 TAGTGACCAAAAGGCAGGTG 57.730 50.000 0.00 0.00 38.50 4.00
2113 2183 1.109323 AGTGACCAAAAGGCAGGTGC 61.109 55.000 0.00 0.00 38.50 5.01
2130 2200 3.267974 CCTTTGAGGCACCGAAGC 58.732 61.111 0.00 0.00 0.00 3.86
2131 2201 1.302832 CCTTTGAGGCACCGAAGCT 60.303 57.895 0.00 0.00 34.17 3.74
2132 2202 1.580845 CCTTTGAGGCACCGAAGCTG 61.581 60.000 0.00 0.00 34.17 4.24
2133 2203 2.192608 CTTTGAGGCACCGAAGCTGC 62.193 60.000 0.00 0.00 34.17 5.25
2154 2224 1.080772 CCGCGCAAGAGTCACAGTA 60.081 57.895 8.75 0.00 43.02 2.74
2186 2256 5.728471 AGGTTCATATAGCTGGAATCGATG 58.272 41.667 0.00 0.00 0.00 3.84
2211 2281 3.350833 GCCATAGGCTCTATCCCATTTG 58.649 50.000 0.00 0.00 46.69 2.32
2240 2310 4.290622 CAGCCCAAGGTGCCCACT 62.291 66.667 0.00 0.00 34.14 4.00
2246 2316 1.656818 CCAAGGTGCCCACTAATGCG 61.657 60.000 0.00 0.00 0.00 4.73
2403 2504 3.197766 TCTTATTCTCATGAGTTGGGCGT 59.802 43.478 21.92 4.90 0.00 5.68
2420 2521 2.097466 GGCGTTTGTCCACCATGAATAG 59.903 50.000 0.00 0.00 0.00 1.73
2466 2568 3.194005 AGAGAGAGAAGACCGAGCTAG 57.806 52.381 0.00 0.00 0.00 3.42
2469 2571 1.098712 AGAGAAGACCGAGCTAGCCG 61.099 60.000 12.13 14.45 0.00 5.52
2508 2616 8.218423 TCTCATGGATACTCTCTATCTCTCTT 57.782 38.462 0.00 0.00 37.61 2.85
2537 3582 4.379339 TTTTCTTTGTTTCGGTTCCTGG 57.621 40.909 0.00 0.00 0.00 4.45
2544 3590 0.322456 TTTCGGTTCCTGGCATGAGG 60.322 55.000 0.00 0.00 0.00 3.86
2562 3608 3.772572 TGAGGAACCGAGAATATGGACAA 59.227 43.478 0.00 0.00 0.00 3.18
2587 3634 9.995003 AAGCCATCTATGTTGTTTTTCATTTTA 57.005 25.926 0.00 0.00 0.00 1.52
2635 3683 1.954146 GCAAGAAGTGGACGCGTGA 60.954 57.895 20.70 0.00 0.00 4.35
2649 3699 0.882474 GCGTGAGGTACAGTGACTCT 59.118 55.000 0.00 0.00 32.58 3.24
2650 3700 1.135632 GCGTGAGGTACAGTGACTCTC 60.136 57.143 0.00 0.90 32.58 3.20
2656 3706 1.134670 GGTACAGTGACTCTCCATGGC 60.135 57.143 6.96 0.00 0.00 4.40
2707 3757 1.444119 CGGGGTGAACAGTTGTGGTG 61.444 60.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.793252 CCAGATGTCTTCCATTTATTTTAGTTG 57.207 33.333 0.00 0.00 32.56 3.16
1 2 9.753674 TCCAGATGTCTTCCATTTATTTTAGTT 57.246 29.630 0.00 0.00 32.56 2.24
2 3 9.401058 CTCCAGATGTCTTCCATTTATTTTAGT 57.599 33.333 0.00 0.00 32.56 2.24
3 4 8.348507 GCTCCAGATGTCTTCCATTTATTTTAG 58.651 37.037 0.00 0.00 32.56 1.85
5 6 6.664816 TGCTCCAGATGTCTTCCATTTATTTT 59.335 34.615 0.00 0.00 32.56 1.82
6 7 6.189859 TGCTCCAGATGTCTTCCATTTATTT 58.810 36.000 0.00 0.00 32.56 1.40
7 8 5.759059 TGCTCCAGATGTCTTCCATTTATT 58.241 37.500 0.00 0.00 32.56 1.40
8 9 5.378230 TGCTCCAGATGTCTTCCATTTAT 57.622 39.130 0.00 0.00 32.56 1.40
9 10 4.842531 TGCTCCAGATGTCTTCCATTTA 57.157 40.909 0.00 0.00 32.56 1.40
10 11 3.726557 TGCTCCAGATGTCTTCCATTT 57.273 42.857 0.00 0.00 32.56 2.32
12 13 2.224233 CGATGCTCCAGATGTCTTCCAT 60.224 50.000 0.00 0.00 36.13 3.41
13 14 1.137675 CGATGCTCCAGATGTCTTCCA 59.862 52.381 0.00 0.00 0.00 3.53
14 15 1.539929 CCGATGCTCCAGATGTCTTCC 60.540 57.143 0.00 0.00 0.00 3.46
15 16 1.137872 ACCGATGCTCCAGATGTCTTC 59.862 52.381 0.00 0.00 0.00 2.87
16 17 1.137872 GACCGATGCTCCAGATGTCTT 59.862 52.381 0.00 0.00 0.00 3.01
17 18 0.749649 GACCGATGCTCCAGATGTCT 59.250 55.000 0.00 0.00 0.00 3.41
18 19 0.749649 AGACCGATGCTCCAGATGTC 59.250 55.000 0.00 0.00 0.00 3.06
19 20 0.749649 GAGACCGATGCTCCAGATGT 59.250 55.000 0.00 0.00 0.00 3.06
20 21 0.318529 CGAGACCGATGCTCCAGATG 60.319 60.000 0.00 0.00 38.22 2.90
21 22 1.459455 CCGAGACCGATGCTCCAGAT 61.459 60.000 0.00 0.00 38.22 2.90
22 23 2.121538 CCGAGACCGATGCTCCAGA 61.122 63.158 0.00 0.00 38.22 3.86
23 24 2.415010 CCGAGACCGATGCTCCAG 59.585 66.667 0.00 0.00 38.22 3.86
24 25 3.147595 CCCGAGACCGATGCTCCA 61.148 66.667 0.00 0.00 38.22 3.86
25 26 3.917760 CCCCGAGACCGATGCTCC 61.918 72.222 0.00 0.00 38.22 4.70
26 27 4.593864 GCCCCGAGACCGATGCTC 62.594 72.222 0.00 0.00 38.22 4.26
29 30 2.777972 TAACGCCCCGAGACCGATG 61.778 63.158 0.00 0.00 38.22 3.84
30 31 2.440796 TAACGCCCCGAGACCGAT 60.441 61.111 0.00 0.00 38.22 4.18
31 32 3.443045 GTAACGCCCCGAGACCGA 61.443 66.667 0.00 0.00 38.22 4.69
32 33 3.751246 TGTAACGCCCCGAGACCG 61.751 66.667 0.00 0.00 0.00 4.79
33 34 2.125793 GTGTAACGCCCCGAGACC 60.126 66.667 0.00 0.00 0.00 3.85
44 45 3.265070 ACAGAAGTCTCGACGTGTAAC 57.735 47.619 0.00 0.00 36.20 2.50
45 46 3.120408 GCTACAGAAGTCTCGACGTGTAA 60.120 47.826 0.00 0.00 36.20 2.41
46 47 2.414481 GCTACAGAAGTCTCGACGTGTA 59.586 50.000 0.00 8.59 36.20 2.90
47 48 1.197264 GCTACAGAAGTCTCGACGTGT 59.803 52.381 0.00 7.54 36.20 4.49
48 49 1.197036 TGCTACAGAAGTCTCGACGTG 59.803 52.381 0.00 0.00 36.20 4.49
49 50 1.520494 TGCTACAGAAGTCTCGACGT 58.480 50.000 0.00 0.00 36.20 4.34
50 51 2.243407 GTTGCTACAGAAGTCTCGACG 58.757 52.381 0.00 0.00 36.20 5.12
65 66 1.684248 GCTCCCCTCATCATTGTTGCT 60.684 52.381 0.00 0.00 0.00 3.91
70 71 1.019673 CGTTGCTCCCCTCATCATTG 58.980 55.000 0.00 0.00 0.00 2.82
71 72 0.911769 TCGTTGCTCCCCTCATCATT 59.088 50.000 0.00 0.00 0.00 2.57
88 89 0.603707 ACCATTGCCACACTCTGTCG 60.604 55.000 0.00 0.00 0.00 4.35
90 91 1.133823 TCAACCATTGCCACACTCTGT 60.134 47.619 0.00 0.00 0.00 3.41
92 93 1.546323 CCTCAACCATTGCCACACTCT 60.546 52.381 0.00 0.00 0.00 3.24
93 94 0.883833 CCTCAACCATTGCCACACTC 59.116 55.000 0.00 0.00 0.00 3.51
96 97 1.702401 TCTACCTCAACCATTGCCACA 59.298 47.619 0.00 0.00 0.00 4.17
100 102 1.369625 CCGTCTACCTCAACCATTGC 58.630 55.000 0.00 0.00 0.00 3.56
102 104 1.207329 GAGCCGTCTACCTCAACCATT 59.793 52.381 0.00 0.00 0.00 3.16
119 121 2.507324 GACACGCCGGAGAAGAGC 60.507 66.667 13.83 0.00 0.00 4.09
127 129 3.958147 AATCCTGCAGACACGCCGG 62.958 63.158 17.39 0.00 37.60 6.13
152 154 3.302870 CGACTTCGTAACAACAAACCAGG 60.303 47.826 0.00 0.00 34.11 4.45
160 162 2.409879 GCAGCTTCGACTTCGTAACAAC 60.410 50.000 0.00 0.00 40.80 3.32
166 168 2.430921 CCGCAGCTTCGACTTCGT 60.431 61.111 7.52 0.00 40.80 3.85
197 201 1.522806 GCCCGTCATCGTATGCCAA 60.523 57.895 0.00 0.00 35.01 4.52
202 206 1.068083 CTGCTGCCCGTCATCGTAT 59.932 57.895 0.00 0.00 35.01 3.06
217 221 1.234821 TCATCGAACAAACCACCTGC 58.765 50.000 0.00 0.00 0.00 4.85
252 256 1.002087 CAAAGGAGAAGTAGGCACGGT 59.998 52.381 0.00 0.00 0.00 4.83
261 265 5.070981 TGACAGAGAATCACAAAGGAGAAGT 59.929 40.000 0.00 0.00 37.82 3.01
262 266 5.545588 TGACAGAGAATCACAAAGGAGAAG 58.454 41.667 0.00 0.00 37.82 2.85
280 284 2.020720 ACATAGCTCCGACTCTGACAG 58.979 52.381 0.00 0.00 0.00 3.51
281 285 2.130272 ACATAGCTCCGACTCTGACA 57.870 50.000 0.00 0.00 0.00 3.58
297 301 1.273606 CCTGAGACGACCAGACAACAT 59.726 52.381 0.00 0.00 33.65 2.71
298 302 0.673985 CCTGAGACGACCAGACAACA 59.326 55.000 0.00 0.00 33.65 3.33
300 304 0.673985 CACCTGAGACGACCAGACAA 59.326 55.000 0.00 0.00 33.65 3.18
302 306 1.587054 CCACCTGAGACGACCAGAC 59.413 63.158 0.00 0.00 33.65 3.51
303 307 2.276116 GCCACCTGAGACGACCAGA 61.276 63.158 0.00 0.00 33.65 3.86
304 308 2.262915 GCCACCTGAGACGACCAG 59.737 66.667 0.00 0.00 0.00 4.00
305 309 2.203640 AGCCACCTGAGACGACCA 60.204 61.111 0.00 0.00 0.00 4.02
306 310 2.262915 CAGCCACCTGAGACGACC 59.737 66.667 0.00 0.00 41.77 4.79
307 311 3.366629 TCAGCCACCTGAGACGAC 58.633 61.111 0.00 0.00 42.98 4.34
313 317 0.764369 ACCAGAACTCAGCCACCTGA 60.764 55.000 0.00 0.00 45.54 3.86
314 318 0.604780 CACCAGAACTCAGCCACCTG 60.605 60.000 0.00 0.00 40.54 4.00
331 335 9.457110 CATGTAGAGATATATAAAGATCCGCAC 57.543 37.037 0.00 0.00 0.00 5.34
332 336 8.633561 CCATGTAGAGATATATAAAGATCCGCA 58.366 37.037 0.00 0.00 0.00 5.69
346 350 6.887002 CACACTATAGAGGCCATGTAGAGATA 59.113 42.308 15.70 0.00 0.00 1.98
352 356 3.923648 ACCACACTATAGAGGCCATGTA 58.076 45.455 5.01 0.00 0.00 2.29
365 369 1.972075 TCATCGACCCAAACCACACTA 59.028 47.619 0.00 0.00 0.00 2.74
373 377 2.639065 GTAGGCAATCATCGACCCAAA 58.361 47.619 0.00 0.00 0.00 3.28
397 401 1.856597 CGAACAAACGACTCCGACTTT 59.143 47.619 0.00 0.00 39.50 2.66
414 418 2.449464 TCGTCATCCCTAAACTCCGAA 58.551 47.619 0.00 0.00 0.00 4.30
417 421 6.097915 TCATAATCGTCATCCCTAAACTCC 57.902 41.667 0.00 0.00 0.00 3.85
430 434 8.552034 CACTTCTTCCCTAAATTCATAATCGTC 58.448 37.037 0.00 0.00 0.00 4.20
436 440 7.110155 GTCACCACTTCTTCCCTAAATTCATA 58.890 38.462 0.00 0.00 0.00 2.15
439 443 5.313712 TGTCACCACTTCTTCCCTAAATTC 58.686 41.667 0.00 0.00 0.00 2.17
440 444 5.319043 TGTCACCACTTCTTCCCTAAATT 57.681 39.130 0.00 0.00 0.00 1.82
441 445 4.993705 TGTCACCACTTCTTCCCTAAAT 57.006 40.909 0.00 0.00 0.00 1.40
443 447 4.349636 TCATTGTCACCACTTCTTCCCTAA 59.650 41.667 0.00 0.00 0.00 2.69
470 474 0.504384 CTCGCGAAGACAACACACAG 59.496 55.000 11.33 0.00 0.00 3.66
490 494 1.178276 CAGACCACTCTAGCGAAGGT 58.822 55.000 2.10 2.10 44.89 3.50
492 496 1.734047 GCACAGACCACTCTAGCGAAG 60.734 57.143 0.00 0.00 0.00 3.79
493 497 0.243907 GCACAGACCACTCTAGCGAA 59.756 55.000 0.00 0.00 0.00 4.70
497 501 0.965866 TCCCGCACAGACCACTCTAG 60.966 60.000 0.00 0.00 0.00 2.43
499 503 0.324368 TATCCCGCACAGACCACTCT 60.324 55.000 0.00 0.00 0.00 3.24
524 528 2.131972 CACAACTGCTAAGCGTACACA 58.868 47.619 0.00 0.00 0.00 3.72
529 533 2.455674 TCATCACAACTGCTAAGCGT 57.544 45.000 0.00 0.00 0.00 5.07
534 539 7.759489 AAGGTAAAAATCATCACAACTGCTA 57.241 32.000 0.00 0.00 0.00 3.49
555 560 4.215613 GCTCAGCCCGGTTAATTATAAAGG 59.784 45.833 0.00 0.00 0.00 3.11
559 570 4.131596 GTTGCTCAGCCCGGTTAATTATA 58.868 43.478 0.00 0.00 0.00 0.98
578 621 8.207545 AGGATTCCTGCTATTAAGAAGTAGTTG 58.792 37.037 3.86 0.00 29.57 3.16
584 627 9.956640 AATGATAGGATTCCTGCTATTAAGAAG 57.043 33.333 15.80 0.00 36.28 2.85
587 630 9.956640 AGAAATGATAGGATTCCTGCTATTAAG 57.043 33.333 15.80 0.00 36.28 1.85
588 631 9.950496 GAGAAATGATAGGATTCCTGCTATTAA 57.050 33.333 15.80 0.00 36.28 1.40
592 642 5.775195 TCGAGAAATGATAGGATTCCTGCTA 59.225 40.000 15.80 1.52 34.61 3.49
593 643 4.590647 TCGAGAAATGATAGGATTCCTGCT 59.409 41.667 15.80 2.37 34.61 4.24
597 647 7.553881 TTTGTTCGAGAAATGATAGGATTCC 57.446 36.000 0.00 0.00 0.00 3.01
623 673 0.603569 CTACTGACGCCCACTGTCTT 59.396 55.000 0.00 0.00 37.26 3.01
627 677 2.507102 CGCTACTGACGCCCACTG 60.507 66.667 0.00 0.00 0.00 3.66
628 678 2.675423 TCGCTACTGACGCCCACT 60.675 61.111 0.00 0.00 0.00 4.00
819 869 3.118592 GGAAAGTGAGGCTGCTATGTACT 60.119 47.826 0.00 0.00 0.00 2.73
849 899 4.157105 AGAAGCCGAGAAGAAACTAGTCTC 59.843 45.833 0.00 0.00 35.47 3.36
853 903 4.712122 AGAGAAGCCGAGAAGAAACTAG 57.288 45.455 0.00 0.00 0.00 2.57
893 948 7.873505 GGTATGAGTGGTGAAGGAAGAATATAC 59.126 40.741 0.00 0.00 0.00 1.47
913 968 2.369203 TGGGTTTGTTGTCTCGGTATGA 59.631 45.455 0.00 0.00 0.00 2.15
1028 1083 1.000270 AGCAGAGAAGAGGCGGAGA 60.000 57.895 0.00 0.00 0.00 3.71
1039 1094 1.270839 CGGAAAAAGGGTGAGCAGAGA 60.271 52.381 0.00 0.00 0.00 3.10
1823 1892 6.127730 TGCACACAGAATAGATTCTCGTCTTA 60.128 38.462 1.66 0.00 44.84 2.10
1824 1893 5.105752 GCACACAGAATAGATTCTCGTCTT 58.894 41.667 1.66 0.00 44.84 3.01
1825 1894 4.158579 TGCACACAGAATAGATTCTCGTCT 59.841 41.667 1.66 0.00 44.84 4.18
1826 1895 4.266502 GTGCACACAGAATAGATTCTCGTC 59.733 45.833 13.17 0.00 44.84 4.20
1827 1896 4.177026 GTGCACACAGAATAGATTCTCGT 58.823 43.478 13.17 0.76 44.84 4.18
1828 1897 3.553511 GGTGCACACAGAATAGATTCTCG 59.446 47.826 20.43 0.18 44.84 4.04
1835 1904 2.479566 AGTGGGTGCACACAGAATAG 57.520 50.000 25.14 0.00 43.72 1.73
1849 1918 2.702592 TTATGGTCCGCTAAAGTGGG 57.297 50.000 9.62 0.00 45.45 4.61
1873 1942 2.607187 CGCTTCCGTGTATCAAAGTCT 58.393 47.619 0.00 0.00 0.00 3.24
1874 1943 1.659098 CCGCTTCCGTGTATCAAAGTC 59.341 52.381 0.00 0.00 0.00 3.01
1875 1944 1.274167 TCCGCTTCCGTGTATCAAAGT 59.726 47.619 0.00 0.00 0.00 2.66
1876 1945 2.004583 TCCGCTTCCGTGTATCAAAG 57.995 50.000 0.00 0.00 0.00 2.77
1877 1946 2.684001 ATCCGCTTCCGTGTATCAAA 57.316 45.000 0.00 0.00 0.00 2.69
1878 1947 2.684001 AATCCGCTTCCGTGTATCAA 57.316 45.000 0.00 0.00 0.00 2.57
1879 1948 2.684001 AAATCCGCTTCCGTGTATCA 57.316 45.000 0.00 0.00 0.00 2.15
1880 1949 4.807304 TCTAAAAATCCGCTTCCGTGTATC 59.193 41.667 0.00 0.00 0.00 2.24
1881 1950 4.761975 TCTAAAAATCCGCTTCCGTGTAT 58.238 39.130 0.00 0.00 0.00 2.29
1882 1951 4.178540 CTCTAAAAATCCGCTTCCGTGTA 58.821 43.478 0.00 0.00 0.00 2.90
1883 1952 3.000727 CTCTAAAAATCCGCTTCCGTGT 58.999 45.455 0.00 0.00 0.00 4.49
1884 1953 2.223044 GCTCTAAAAATCCGCTTCCGTG 60.223 50.000 0.00 0.00 0.00 4.94
1885 1954 2.007608 GCTCTAAAAATCCGCTTCCGT 58.992 47.619 0.00 0.00 0.00 4.69
1886 1955 2.006888 TGCTCTAAAAATCCGCTTCCG 58.993 47.619 0.00 0.00 0.00 4.30
1918 1987 1.071471 GACGGCCATGATACCAGGG 59.929 63.158 2.24 0.00 46.44 4.45
1923 1993 0.529773 TGAAGCGACGGCCATGATAC 60.530 55.000 2.24 0.00 41.24 2.24
1987 2057 5.283294 TGCGCTAAATACTGCTAATAACGA 58.717 37.500 9.73 0.00 0.00 3.85
2000 2070 5.773680 AGTATAGTCCCTCTTGCGCTAAATA 59.226 40.000 9.73 0.00 0.00 1.40
2004 2074 3.225177 AGTATAGTCCCTCTTGCGCTA 57.775 47.619 9.73 0.00 0.00 4.26
2005 2075 2.074729 AGTATAGTCCCTCTTGCGCT 57.925 50.000 9.73 0.00 0.00 5.92
2006 2076 2.745102 GAAGTATAGTCCCTCTTGCGC 58.255 52.381 0.00 0.00 0.00 6.09
2007 2077 2.287668 CCGAAGTATAGTCCCTCTTGCG 60.288 54.545 0.00 0.00 0.00 4.85
2008 2078 2.694109 ACCGAAGTATAGTCCCTCTTGC 59.306 50.000 0.00 0.00 0.00 4.01
2009 2079 3.491104 GCACCGAAGTATAGTCCCTCTTG 60.491 52.174 0.00 0.00 0.00 3.02
2010 2080 2.694109 GCACCGAAGTATAGTCCCTCTT 59.306 50.000 0.00 0.00 0.00 2.85
2011 2081 2.308690 GCACCGAAGTATAGTCCCTCT 58.691 52.381 0.00 0.00 0.00 3.69
2012 2082 1.340568 GGCACCGAAGTATAGTCCCTC 59.659 57.143 0.00 0.00 0.00 4.30
2013 2083 1.063114 AGGCACCGAAGTATAGTCCCT 60.063 52.381 0.00 0.00 0.00 4.20
2014 2084 1.411041 AGGCACCGAAGTATAGTCCC 58.589 55.000 0.00 0.00 0.00 4.46
2015 2085 4.501058 CCTTAAGGCACCGAAGTATAGTCC 60.501 50.000 9.00 0.00 0.00 3.85
2016 2086 4.618965 CCTTAAGGCACCGAAGTATAGTC 58.381 47.826 9.00 0.00 0.00 2.59
2017 2087 4.667519 CCTTAAGGCACCGAAGTATAGT 57.332 45.455 9.00 0.00 0.00 2.12
2034 2104 9.840236 GTCATAGACACAAAGGAAGGTGCCTTA 62.840 44.444 3.11 0.00 38.65 2.69
2036 2106 0.846693 AGACACAAAGGAAGGTGCCT 59.153 50.000 0.00 0.00 40.93 4.75
2037 2107 2.561478 TAGACACAAAGGAAGGTGCC 57.439 50.000 0.00 0.00 38.57 5.01
2038 2108 3.437049 GTCATAGACACAAAGGAAGGTGC 59.563 47.826 0.00 0.00 38.57 5.01
2039 2109 4.641396 TGTCATAGACACAAAGGAAGGTG 58.359 43.478 0.00 0.00 37.67 4.00
2040 2110 4.974645 TGTCATAGACACAAAGGAAGGT 57.025 40.909 0.00 0.00 37.67 3.50
2041 2111 5.122869 CACATGTCATAGACACAAAGGAAGG 59.877 44.000 0.00 0.00 45.65 3.46
2042 2112 5.122869 CCACATGTCATAGACACAAAGGAAG 59.877 44.000 0.00 0.00 45.65 3.46
2043 2113 5.003160 CCACATGTCATAGACACAAAGGAA 58.997 41.667 0.00 0.00 45.65 3.36
2044 2114 4.565444 CCCACATGTCATAGACACAAAGGA 60.565 45.833 0.00 0.00 45.65 3.36
2045 2115 3.691118 CCCACATGTCATAGACACAAAGG 59.309 47.826 0.00 3.02 45.65 3.11
2046 2116 3.127548 GCCCACATGTCATAGACACAAAG 59.872 47.826 0.00 0.00 45.65 2.77
2047 2117 3.081061 GCCCACATGTCATAGACACAAA 58.919 45.455 0.00 0.00 45.65 2.83
2048 2118 2.617788 GGCCCACATGTCATAGACACAA 60.618 50.000 0.00 0.00 45.65 3.33
2049 2119 1.065491 GGCCCACATGTCATAGACACA 60.065 52.381 0.00 0.00 45.65 3.72
2050 2120 1.668419 GGCCCACATGTCATAGACAC 58.332 55.000 0.00 0.00 45.65 3.67
2051 2121 0.546122 GGGCCCACATGTCATAGACA 59.454 55.000 19.95 1.95 46.90 3.41
2052 2122 0.546122 TGGGCCCACATGTCATAGAC 59.454 55.000 24.45 0.00 0.00 2.59
2053 2123 1.064758 GTTGGGCCCACATGTCATAGA 60.065 52.381 28.70 1.58 0.00 1.98
2054 2124 1.340893 TGTTGGGCCCACATGTCATAG 60.341 52.381 28.70 0.00 0.00 2.23
2055 2125 0.701147 TGTTGGGCCCACATGTCATA 59.299 50.000 28.70 3.51 0.00 2.15
2056 2126 0.612732 CTGTTGGGCCCACATGTCAT 60.613 55.000 28.70 0.00 0.00 3.06
2057 2127 1.228521 CTGTTGGGCCCACATGTCA 60.229 57.895 28.70 17.15 0.00 3.58
2058 2128 1.978617 CCTGTTGGGCCCACATGTC 60.979 63.158 28.70 13.28 0.00 3.06
2059 2129 2.118076 CCTGTTGGGCCCACATGT 59.882 61.111 28.70 0.00 0.00 3.21
2060 2130 2.118076 ACCTGTTGGGCCCACATG 59.882 61.111 28.70 23.07 39.10 3.21
2061 2131 2.118076 CACCTGTTGGGCCCACAT 59.882 61.111 28.70 9.27 39.10 3.21
2062 2132 4.217210 CCACCTGTTGGGCCCACA 62.217 66.667 28.70 23.95 42.54 4.17
2070 2140 4.601794 TGGGCCAGCCACCTGTTG 62.602 66.667 11.50 0.00 37.38 3.33
2071 2141 4.603535 GTGGGCCAGCCACCTGTT 62.604 66.667 6.40 0.00 37.38 3.16
2073 2143 4.371417 ATGTGGGCCAGCCACCTG 62.371 66.667 6.40 0.00 37.38 4.00
2074 2144 4.371417 CATGTGGGCCAGCCACCT 62.371 66.667 6.40 0.00 37.38 4.00
2075 2145 2.779742 TAACATGTGGGCCAGCCACC 62.780 60.000 6.40 0.00 37.38 4.61
2076 2146 1.304052 TAACATGTGGGCCAGCCAC 60.304 57.895 6.40 4.05 37.98 5.01
2077 2147 1.001020 CTAACATGTGGGCCAGCCA 60.001 57.895 6.40 1.84 37.98 4.75
2078 2148 1.000896 ACTAACATGTGGGCCAGCC 60.001 57.895 6.40 0.00 0.00 4.85
2079 2149 0.322456 TCACTAACATGTGGGCCAGC 60.322 55.000 6.40 2.28 38.40 4.85
2080 2150 1.453155 GTCACTAACATGTGGGCCAG 58.547 55.000 6.40 0.00 38.40 4.85
2081 2151 0.037590 GGTCACTAACATGTGGGCCA 59.962 55.000 0.00 0.00 38.40 5.36
2082 2152 0.037590 TGGTCACTAACATGTGGGCC 59.962 55.000 0.00 0.00 38.40 5.80
2083 2153 1.904287 TTGGTCACTAACATGTGGGC 58.096 50.000 0.00 0.00 38.40 5.36
2084 2154 3.255642 CCTTTTGGTCACTAACATGTGGG 59.744 47.826 0.00 0.00 38.40 4.61
2085 2155 3.305335 GCCTTTTGGTCACTAACATGTGG 60.305 47.826 0.00 0.00 42.99 4.17
2086 2156 3.317711 TGCCTTTTGGTCACTAACATGTG 59.682 43.478 0.00 0.00 42.99 3.21
2087 2157 3.561143 TGCCTTTTGGTCACTAACATGT 58.439 40.909 0.00 0.00 42.99 3.21
2088 2158 3.057315 CCTGCCTTTTGGTCACTAACATG 60.057 47.826 0.00 0.00 42.99 3.21
2089 2159 3.157087 CCTGCCTTTTGGTCACTAACAT 58.843 45.455 0.00 0.00 42.99 2.71
2090 2160 2.092103 ACCTGCCTTTTGGTCACTAACA 60.092 45.455 0.00 0.00 42.99 2.41
2091 2161 2.293399 CACCTGCCTTTTGGTCACTAAC 59.707 50.000 0.00 0.00 42.99 2.34
2092 2162 2.582052 CACCTGCCTTTTGGTCACTAA 58.418 47.619 0.00 0.00 42.99 2.24
2093 2163 1.817740 GCACCTGCCTTTTGGTCACTA 60.818 52.381 0.00 0.00 42.99 2.74
2094 2164 1.109323 GCACCTGCCTTTTGGTCACT 61.109 55.000 0.00 0.00 42.99 3.41
2095 2165 1.363807 GCACCTGCCTTTTGGTCAC 59.636 57.895 0.00 0.00 42.99 3.67
2096 2166 3.854856 GCACCTGCCTTTTGGTCA 58.145 55.556 0.00 0.00 42.99 4.02
2113 2183 1.302832 AGCTTCGGTGCCTCAAAGG 60.303 57.895 0.00 0.00 38.80 3.11
2114 2184 1.871772 CAGCTTCGGTGCCTCAAAG 59.128 57.895 0.00 0.00 0.00 2.77
2115 2185 4.063529 CAGCTTCGGTGCCTCAAA 57.936 55.556 0.00 0.00 0.00 2.69
2133 2203 3.470567 GTGACTCTTGCGCGGACG 61.471 66.667 8.83 1.84 44.07 4.79
2134 2204 2.355837 TGTGACTCTTGCGCGGAC 60.356 61.111 8.83 0.00 0.00 4.79
2135 2205 1.520600 TACTGTGACTCTTGCGCGGA 61.521 55.000 8.83 0.00 0.00 5.54
2136 2206 1.073216 CTACTGTGACTCTTGCGCGG 61.073 60.000 8.83 0.00 0.00 6.46
2137 2207 1.073216 CCTACTGTGACTCTTGCGCG 61.073 60.000 0.00 0.00 0.00 6.86
2154 2224 5.046014 CCAGCTATATGAACCTATGAAGCCT 60.046 44.000 0.00 0.00 0.00 4.58
2202 2272 3.390639 TGCAGAACAAAACCAAATGGGAT 59.609 39.130 4.17 0.00 41.15 3.85
2211 2281 0.463620 TTGGGCTGCAGAACAAAACC 59.536 50.000 20.43 6.83 0.00 3.27
2240 2310 3.498777 TGTCGTTTCCATTGTTCGCATTA 59.501 39.130 0.00 0.00 0.00 1.90
2246 2316 2.875933 TGGACTGTCGTTTCCATTGTTC 59.124 45.455 1.07 0.00 36.96 3.18
2384 2485 3.627395 AACGCCCAACTCATGAGAATA 57.373 42.857 29.27 0.00 0.00 1.75
2403 2504 5.887598 CCATCTTCTATTCATGGTGGACAAA 59.112 40.000 0.00 0.00 33.57 2.83
2466 2568 3.145422 GAGTCCAGCTAGAGCCGGC 62.145 68.421 21.89 21.89 43.38 6.13
2469 2571 1.340889 CATGAGAGTCCAGCTAGAGCC 59.659 57.143 0.00 0.00 43.38 4.70
2508 2616 7.255001 GGAACCGAAACAAAGAAAATGAGAGTA 60.255 37.037 0.00 0.00 0.00 2.59
2537 3582 3.070018 CCATATTCTCGGTTCCTCATGC 58.930 50.000 0.00 0.00 0.00 4.06
2544 3590 2.872858 GGCTTGTCCATATTCTCGGTTC 59.127 50.000 0.00 0.00 34.01 3.62
2562 3608 9.995003 TTAAAATGAAAAACAACATAGATGGCT 57.005 25.926 0.00 0.00 0.00 4.75
2587 3634 6.380846 TGCTCTTTCTATTGCCCATGTTTATT 59.619 34.615 0.00 0.00 0.00 1.40
2595 3642 3.614092 CTCTTGCTCTTTCTATTGCCCA 58.386 45.455 0.00 0.00 0.00 5.36
2597 3644 2.357323 GCCTCTTGCTCTTTCTATTGCC 59.643 50.000 0.00 0.00 36.87 4.52
2603 3650 3.181446 ACTTCTTGCCTCTTGCTCTTTCT 60.181 43.478 0.00 0.00 42.00 2.52
2635 3683 2.461695 CCATGGAGAGTCACTGTACCT 58.538 52.381 5.56 0.00 0.00 3.08
2649 3699 3.903090 ACAAATTTCTTGGAAGCCATGGA 59.097 39.130 18.40 0.00 31.53 3.41
2650 3700 4.020839 AGACAAATTTCTTGGAAGCCATGG 60.021 41.667 7.63 7.63 31.53 3.66
2656 3706 4.614535 CGAGCCAGACAAATTTCTTGGAAG 60.615 45.833 13.61 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.