Multiple sequence alignment - TraesCS2D01G154800

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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 TraesCS2D01G154800 chr2D 100.000 5272 0 0 1 5272 98271285 98266014 0.000000e+00 9736.0
1 TraesCS2D01G154800 chr2D 91.667 96 8 0 2168 2263 54674230 54674325 3.310000e-27 134.0
2 TraesCS2D01G154800 chr2D 92.391 92 7 0 2176 2267 164992681 164992772 1.190000e-26 132.0
3 TraesCS2D01G154800 chr2B 93.288 4693 204 53 1 4662 149846958 149842346 0.000000e+00 6818.0
4 TraesCS2D01G154800 chr2B 86.222 225 18 4 4815 5027 149842123 149841900 1.140000e-56 231.0
5 TraesCS2D01G154800 chr2B 93.805 113 5 1 5058 5168 149841905 149841793 9.080000e-38 169.0
6 TraesCS2D01G154800 chr2B 93.578 109 7 0 5164 5272 149841755 149841647 4.220000e-36 163.0
7 TraesCS2D01G154800 chr2B 90.909 99 9 0 2171 2269 387076280 387076182 3.310000e-27 134.0
8 TraesCS2D01G154800 chr2B 97.436 39 1 0 708 746 28788945 28788983 3.410000e-07 67.6
9 TraesCS2D01G154800 chr2A 93.059 2579 134 23 2265 4821 96250423 96247868 0.000000e+00 3729.0
10 TraesCS2D01G154800 chr2A 95.662 1337 41 7 855 2177 96251765 96250432 0.000000e+00 2132.0
11 TraesCS2D01G154800 chr2A 86.842 380 21 11 4815 5180 96247845 96247481 1.060000e-106 398.0
12 TraesCS2D01G154800 chr2A 95.413 109 5 0 5164 5272 96247452 96247344 1.950000e-39 174.0
13 TraesCS2D01G154800 chr2A 85.093 161 17 6 4654 4809 6185294 6185136 1.970000e-34 158.0
14 TraesCS2D01G154800 chr2A 85.000 160 17 6 4654 4808 6134247 6134090 7.070000e-34 156.0
15 TraesCS2D01G154800 chr2A 92.784 97 6 1 2175 2270 115434414 115434510 7.120000e-29 139.0
16 TraesCS2D01G154800 chr7A 82.427 478 54 19 2012 2470 138739386 138739852 1.780000e-104 390.0
17 TraesCS2D01G154800 chr7A 77.037 405 47 20 4598 4962 13114113 13113715 1.940000e-44 191.0
18 TraesCS2D01G154800 chr7A 84.375 128 9 9 601 721 244575573 244575696 1.200000e-21 115.0
19 TraesCS2D01G154800 chr7D 81.895 475 56 19 2015 2470 424268444 424267981 1.790000e-99 374.0
20 TraesCS2D01G154800 chr7D 91.000 100 8 1 2171 2270 519264638 519264540 3.310000e-27 134.0
21 TraesCS2D01G154800 chr7B 81.687 486 54 22 2015 2479 326671377 326670906 6.450000e-99 372.0
22 TraesCS2D01G154800 chr4D 81.316 471 58 21 2019 2470 503868827 503868368 6.490000e-94 355.0
23 TraesCS2D01G154800 chr4D 86.508 126 9 6 613 731 31802995 31803119 1.190000e-26 132.0
24 TraesCS2D01G154800 chr6D 79.372 446 62 21 324 746 248515686 248516124 2.400000e-73 287.0
25 TraesCS2D01G154800 chr6D 83.673 147 17 5 4816 4962 460563657 460563796 1.190000e-26 132.0
26 TraesCS2D01G154800 chr5B 87.919 149 15 3 4815 4962 593471153 593471007 7.020000e-39 172.0
27 TraesCS2D01G154800 chr5B 83.243 185 25 4 4600 4778 141580255 141580439 1.170000e-36 165.0
28 TraesCS2D01G154800 chr5B 78.761 226 33 11 4601 4815 491115767 491115988 2.560000e-28 137.0
29 TraesCS2D01G154800 chr5B 83.099 142 21 2 4816 4957 9285448 9285310 5.540000e-25 126.0
30 TraesCS2D01G154800 chr5B 80.952 147 23 4 4819 4962 351496836 351496692 1.550000e-20 111.0
31 TraesCS2D01G154800 chr4B 84.706 170 24 2 4610 4778 653208049 653208217 9.080000e-38 169.0
32 TraesCS2D01G154800 chr4B 92.784 97 6 1 2175 2270 438099357 438099453 7.120000e-29 139.0
33 TraesCS2D01G154800 chr1D 85.366 164 18 4 4653 4810 419071807 419071644 1.170000e-36 165.0
34 TraesCS2D01G154800 chr1D 81.308 214 25 8 4601 4800 296736156 296736368 5.460000e-35 159.0
35 TraesCS2D01G154800 chr1D 86.508 126 9 6 601 720 14741082 14741205 1.190000e-26 132.0
36 TraesCS2D01G154800 chr6B 85.333 150 22 0 4818 4967 449454368 449454219 7.070000e-34 156.0
37 TraesCS2D01G154800 chr6B 84.375 128 11 7 601 721 585817008 585817133 3.340000e-22 117.0
38 TraesCS2D01G154800 chr4A 81.319 182 24 8 4604 4779 744045519 744045696 7.120000e-29 139.0
39 TraesCS2D01G154800 chr3B 84.173 139 22 0 4819 4957 704257833 704257695 9.210000e-28 135.0
40 TraesCS2D01G154800 chr3B 85.401 137 11 8 601 731 482988882 482988749 3.310000e-27 134.0
41 TraesCS2D01G154800 chr1B 91.837 98 6 1 2175 2270 93954294 93954391 9.210000e-28 135.0
42 TraesCS2D01G154800 chr1B 80.978 184 24 8 4695 4871 497265954 497265775 9.210000e-28 135.0
43 TraesCS2D01G154800 chr3D 92.473 93 7 0 2171 2263 303788549 303788457 3.310000e-27 134.0
44 TraesCS2D01G154800 chr3D 87.963 108 10 3 2173 2278 526509388 526509282 1.990000e-24 124.0
45 TraesCS2D01G154800 chr1A 86.508 126 8 8 601 720 251347894 251347772 4.280000e-26 130.0
46 TraesCS2D01G154800 chr3A 82.237 152 19 6 601 746 718561535 718561684 1.990000e-24 124.0
47 TraesCS2D01G154800 chr3A 80.405 148 23 6 4817 4958 688530066 688529919 2.010000e-19 108.0
48 TraesCS2D01G154800 chrUn 79.618 157 19 9 4816 4963 272114484 272114332 3.360000e-17 100.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G154800 chr2D 98266014 98271285 5271 True 9736.00 9736 100.00000 1 5272 1 chr2D.!!$R1 5271
1 TraesCS2D01G154800 chr2B 149841647 149846958 5311 True 1845.25 6818 91.72325 1 5272 4 chr2B.!!$R2 5271
2 TraesCS2D01G154800 chr2A 96247344 96251765 4421 True 1608.25 3729 92.74400 855 5272 4 chr2A.!!$R3 4417

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
546 547 0.611896 ATAACTTTTGCCCCGCAGCT 60.612 50.0 0.00 0.0 40.61 4.24 F
1532 1547 0.468226 TCTTGGTGTTGAAGACGGCT 59.532 50.0 0.00 0.0 0.00 5.52 F
2240 2264 1.021968 GTGGTGTCAAAACCGCTCTT 58.978 50.0 0.00 0.0 45.52 2.85 F
3775 3806 0.320771 AAGAGTCCCATGACACGTGC 60.321 55.0 17.22 9.3 44.33 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2220 2244 0.180406 AGAGCGGTTTTGACACCACT 59.820 50.0 0.00 0.00 36.49 4.00 R
3516 3547 1.031235 CCACCACTGAATGTGCACAA 58.969 50.0 25.72 6.58 44.92 3.33 R
4009 4041 0.933097 CGGCATGAGACTTCCATTCG 59.067 55.0 0.00 0.00 0.00 3.34 R
5026 5178 0.038890 TTTGTGGAATCGGATGGCCA 59.961 50.0 8.56 8.56 0.00 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
41 42 0.945813 TTTCACCCTAAAACGTGCCG 59.054 50.000 0.00 0.00 0.00 5.69
45 46 2.043980 CCCTAAAACGTGCCGCCAT 61.044 57.895 0.00 0.00 0.00 4.40
125 126 1.401931 CCGCAAATTTGAGTCTGCCAG 60.402 52.381 22.31 0.31 0.00 4.85
134 135 2.184579 GTCTGCCAGGCCGACTAC 59.815 66.667 24.84 3.31 39.17 2.73
171 172 3.883997 GCGATTTGTGCCTGGAAAA 57.116 47.368 0.00 0.00 0.00 2.29
172 173 1.701704 GCGATTTGTGCCTGGAAAAG 58.298 50.000 0.00 0.00 0.00 2.27
173 174 1.000274 GCGATTTGTGCCTGGAAAAGT 60.000 47.619 0.00 0.00 0.00 2.66
181 182 2.380410 CCTGGAAAAGTCGTCGCCG 61.380 63.158 0.00 0.00 0.00 6.46
219 220 2.657237 GACCCTGTCGTGACCCAG 59.343 66.667 0.00 0.00 0.00 4.45
220 221 3.591254 GACCCTGTCGTGACCCAGC 62.591 68.421 0.00 0.00 0.00 4.85
221 222 3.314331 CCCTGTCGTGACCCAGCT 61.314 66.667 0.00 0.00 0.00 4.24
222 223 2.047844 CCTGTCGTGACCCAGCTG 60.048 66.667 6.78 6.78 0.00 4.24
223 224 2.740055 CTGTCGTGACCCAGCTGC 60.740 66.667 8.66 0.00 0.00 5.25
224 225 4.314440 TGTCGTGACCCAGCTGCC 62.314 66.667 8.66 0.00 0.00 4.85
225 226 4.008933 GTCGTGACCCAGCTGCCT 62.009 66.667 8.66 0.00 0.00 4.75
226 227 2.283604 TCGTGACCCAGCTGCCTA 60.284 61.111 8.66 0.00 0.00 3.93
227 228 1.685765 TCGTGACCCAGCTGCCTAT 60.686 57.895 8.66 0.00 0.00 2.57
231 232 2.765807 ACCCAGCTGCCTATCGCT 60.766 61.111 8.66 0.00 38.78 4.93
264 265 4.063967 CACCGCACCGCTACTCCA 62.064 66.667 0.00 0.00 0.00 3.86
289 290 1.657487 CGCTGCGAATCGACCGTAT 60.657 57.895 18.66 0.00 0.00 3.06
309 310 2.285889 TTTTTCCCGCCCCACTGACA 62.286 55.000 0.00 0.00 0.00 3.58
310 311 2.969300 TTTTCCCGCCCCACTGACAC 62.969 60.000 0.00 0.00 0.00 3.67
321 322 2.280524 CTGACACCGTTTCCGCCA 60.281 61.111 0.00 0.00 0.00 5.69
345 346 4.446413 CCGCCAGTACCCGTCCAC 62.446 72.222 0.00 0.00 0.00 4.02
346 347 4.446413 CGCCAGTACCCGTCCACC 62.446 72.222 0.00 0.00 0.00 4.61
347 348 3.315949 GCCAGTACCCGTCCACCA 61.316 66.667 0.00 0.00 0.00 4.17
416 417 1.011333 ATCGGTTGTATTTTCCGCCG 58.989 50.000 0.00 0.00 43.35 6.46
422 423 1.022451 TGTATTTTCCGCCGCTCCAC 61.022 55.000 0.00 0.00 0.00 4.02
423 424 0.743345 GTATTTTCCGCCGCTCCACT 60.743 55.000 0.00 0.00 0.00 4.00
456 457 3.056328 GTCCCCGCTGCTGTTTCC 61.056 66.667 0.00 0.00 0.00 3.13
457 458 4.697756 TCCCCGCTGCTGTTTCCG 62.698 66.667 0.00 0.00 0.00 4.30
461 462 3.434319 CGCTGCTGTTTCCGCCAT 61.434 61.111 0.00 0.00 0.00 4.40
462 463 2.964978 GCTGCTGTTTCCGCCATT 59.035 55.556 0.00 0.00 0.00 3.16
475 476 3.957535 CCATTGCCGCCGCTCATC 61.958 66.667 0.00 0.00 35.36 2.92
483 484 2.887568 GCCGCTCATCCGTCACTG 60.888 66.667 0.00 0.00 0.00 3.66
494 495 3.357079 GTCACTGCCAAGCCACCG 61.357 66.667 0.00 0.00 0.00 4.94
546 547 0.611896 ATAACTTTTGCCCCGCAGCT 60.612 50.000 0.00 0.00 40.61 4.24
615 621 4.154176 CCCCAATCATCTCCATTTGCATA 58.846 43.478 0.00 0.00 0.00 3.14
648 654 6.072728 GGAGTTGCACTTTTACATCACACATA 60.073 38.462 0.00 0.00 0.00 2.29
653 659 8.109705 TGCACTTTTACATCACACATAATCTT 57.890 30.769 0.00 0.00 0.00 2.40
671 677 5.876651 ATCTTTTGGAGTTGCCTCTTTTT 57.123 34.783 0.00 0.00 37.86 1.94
731 738 7.933033 ACTGTTTTACATCTCCAAATTTGCATT 59.067 29.630 12.92 0.00 0.00 3.56
734 741 9.597999 GTTTTACATCTCCAAATTTGCATTTTC 57.402 29.630 12.92 0.00 29.41 2.29
758 765 3.297134 TGGACATGATTTTAGAGGGGC 57.703 47.619 0.00 0.00 0.00 5.80
759 766 2.091885 TGGACATGATTTTAGAGGGGCC 60.092 50.000 0.00 0.00 0.00 5.80
773 780 1.191535 GGGGCCAAATTTACCCAGTC 58.808 55.000 23.33 8.43 46.21 3.51
774 781 1.191535 GGGCCAAATTTACCCAGTCC 58.808 55.000 19.15 2.38 43.64 3.85
776 783 0.815095 GCCAAATTTACCCAGTCCGG 59.185 55.000 0.00 0.00 0.00 5.14
781 788 3.512219 AATTTACCCAGTCCGGTTTCA 57.488 42.857 0.00 0.00 37.34 2.69
851 861 0.803768 CGTGGTTCCAGATGCTCTCG 60.804 60.000 0.00 0.00 0.00 4.04
978 993 2.231380 ACGACTCCAGCCCCCAAAT 61.231 57.895 0.00 0.00 0.00 2.32
1280 1295 3.062042 GGAGTACCAATTTCGTTCGTGT 58.938 45.455 0.00 0.00 35.97 4.49
1330 1345 1.674441 ACTGGCATCAGATTTCGCATG 59.326 47.619 0.00 0.00 43.49 4.06
1511 1526 1.153549 GAGGGAGTGCAAGCGGTAG 60.154 63.158 0.00 0.00 0.00 3.18
1518 1533 1.003839 TGCAAGCGGTAGGTCTTGG 60.004 57.895 4.45 0.00 39.87 3.61
1520 1535 1.298859 GCAAGCGGTAGGTCTTGGTG 61.299 60.000 4.45 0.00 39.87 4.17
1522 1537 0.763035 AAGCGGTAGGTCTTGGTGTT 59.237 50.000 0.00 0.00 0.00 3.32
1526 1541 2.413837 CGGTAGGTCTTGGTGTTGAAG 58.586 52.381 0.00 0.00 0.00 3.02
1529 1544 2.240493 AGGTCTTGGTGTTGAAGACG 57.760 50.000 0.00 0.00 46.98 4.18
1532 1547 0.468226 TCTTGGTGTTGAAGACGGCT 59.532 50.000 0.00 0.00 0.00 5.52
1535 1550 2.851263 TGGTGTTGAAGACGGCTATT 57.149 45.000 0.00 0.00 0.00 1.73
1596 1619 2.994578 TGTGGCATGATGAAATTTTGCG 59.005 40.909 0.00 0.00 35.94 4.85
1597 1620 2.349275 GTGGCATGATGAAATTTTGCGG 59.651 45.455 0.00 0.00 35.94 5.69
1901 1925 6.112384 CCATGAGGAAGACGTGAGTACACA 62.112 50.000 0.00 0.00 41.07 3.72
2032 2056 3.173668 TCCGTCCCATTGTAAATCTCG 57.826 47.619 0.00 0.00 0.00 4.04
2206 2230 5.394663 CCCTCTGTCCCATAATATAAGAGCG 60.395 48.000 0.00 0.00 0.00 5.03
2207 2231 5.186021 CCTCTGTCCCATAATATAAGAGCGT 59.814 44.000 0.00 0.00 0.00 5.07
2220 2244 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
2221 2245 4.795970 AAGAGCGTTTTTGACACTACAG 57.204 40.909 0.00 0.00 0.00 2.74
2222 2246 3.793559 AGAGCGTTTTTGACACTACAGT 58.206 40.909 0.00 0.00 0.00 3.55
2234 2258 3.963383 CACTACAGTGGTGTCAAAACC 57.037 47.619 8.88 0.00 42.10 3.27
2240 2264 1.021968 GTGGTGTCAAAACCGCTCTT 58.978 50.000 0.00 0.00 45.52 2.85
2254 2278 3.830755 ACCGCTCTTATATTATGGGACGT 59.169 43.478 0.00 0.00 0.00 4.34
2322 2346 4.392921 ACATTCTCATCCAAGTACCTCG 57.607 45.455 0.00 0.00 0.00 4.63
2355 2379 6.339730 TGCAGAAATGTCAAATCAACAACTT 58.660 32.000 0.00 0.00 0.00 2.66
2463 2487 8.956426 TCTTTTGTTGTTCACTCTTTCATAAGT 58.044 29.630 0.00 0.00 32.98 2.24
2466 2490 9.997482 TTTGTTGTTCACTCTTTCATAAGTTAC 57.003 29.630 0.00 0.00 32.98 2.50
2486 2510 7.668492 AGTTACTTTTACAGAAGAGTCGGAAT 58.332 34.615 0.00 0.00 32.52 3.01
2700 2724 4.104102 AGTTCAACTGTGGTTCCTATTCCA 59.896 41.667 0.00 0.00 32.73 3.53
2811 2838 7.441157 GGTGTATCGATCAATCTGTATTTTCCA 59.559 37.037 0.00 0.00 0.00 3.53
2932 2963 9.871238 ACTTAAAGAATCTTGTTTATCGCTCTA 57.129 29.630 0.00 0.00 0.00 2.43
3189 3220 4.337555 ACAATGGCTGAGACTTGCAATATC 59.662 41.667 0.00 0.60 0.00 1.63
3315 3346 9.607988 TGTGTTAGTATTTGTATTGGGTATGAG 57.392 33.333 0.00 0.00 0.00 2.90
3500 3531 7.148086 TGGAGATAAAATGTCGGATGAAAAAGG 60.148 37.037 0.00 0.00 0.00 3.11
3704 3735 4.941873 CCTTTGGTAGTTTGGTGGAGATAC 59.058 45.833 0.00 0.00 0.00 2.24
3718 3749 3.519107 TGGAGATACAAATGACTCCTGCA 59.481 43.478 18.34 0.00 46.14 4.41
3775 3806 0.320771 AAGAGTCCCATGACACGTGC 60.321 55.000 17.22 9.30 44.33 5.34
3826 3857 8.328864 CCAAATTGGCAAAACAAAATTTGATTG 58.671 29.630 13.19 16.08 45.99 2.67
3827 3858 9.084164 CAAATTGGCAAAACAAAATTTGATTGA 57.916 25.926 22.69 10.15 45.99 2.57
3828 3859 9.819267 AAATTGGCAAAACAAAATTTGATTGAT 57.181 22.222 22.69 11.40 41.73 2.57
3829 3860 9.819267 AATTGGCAAAACAAAATTTGATTGATT 57.181 22.222 22.69 14.77 41.73 2.57
3830 3861 9.819267 ATTGGCAAAACAAAATTTGATTGATTT 57.181 22.222 22.69 8.56 41.73 2.17
3884 3915 7.148188 TGCAAATGATAATCTGACCTTGTCTTC 60.148 37.037 0.00 0.00 33.15 2.87
3885 3916 7.066766 GCAAATGATAATCTGACCTTGTCTTCT 59.933 37.037 0.00 0.00 33.15 2.85
3886 3917 8.610896 CAAATGATAATCTGACCTTGTCTTCTC 58.389 37.037 0.00 0.00 33.15 2.87
3914 3946 2.423577 GTCAACCCGCATAACAAGAGT 58.576 47.619 0.00 0.00 0.00 3.24
3971 4003 2.125673 GCGCAGAACCGGAAGCTA 60.126 61.111 9.46 0.00 0.00 3.32
4023 4055 3.002791 GCATTCACGAATGGAAGTCTCA 58.997 45.455 18.77 0.00 46.14 3.27
4052 4084 1.599606 GGTCTCTCGCTCTGAAGCCA 61.600 60.000 0.00 0.00 46.34 4.75
4076 4108 2.899976 ACACACGATGTCAACTGTTCA 58.100 42.857 0.00 0.00 36.54 3.18
4189 4221 0.814010 AGCACTTCGGTTGTGTGGTC 60.814 55.000 0.00 0.00 37.84 4.02
4227 4259 2.139917 TCTTGGTTGTGTACATGCGTC 58.860 47.619 0.00 0.00 0.00 5.19
4255 4287 3.951680 TGACCAGTGAGAGTTATGCGATA 59.048 43.478 0.00 0.00 0.00 2.92
4291 4323 1.003233 ACCTTCCTAAAACCAGCCGAG 59.997 52.381 0.00 0.00 0.00 4.63
4337 4369 3.527253 TGTTGTCCATCCATTATCCTGGT 59.473 43.478 0.00 0.00 37.57 4.00
4354 4386 2.929641 TGGTCTTGTGAGCATGTTTCA 58.070 42.857 0.00 0.00 44.58 2.69
4380 4412 3.671008 TCATTTTGCTGCTGAAATGCT 57.329 38.095 24.25 3.77 41.01 3.79
4415 4447 1.351076 TCTGGTGGCAAGATCTGACA 58.649 50.000 0.00 0.00 42.51 3.58
4458 4490 0.846693 AAATCGGGGATAAGCTGGCT 59.153 50.000 0.00 0.00 0.00 4.75
4542 4583 7.458170 AGGTATTGGGGAATAATTCTCGATACT 59.542 37.037 11.75 0.00 34.49 2.12
4549 4590 9.720769 GGGGAATAATTCTCGATACTTATTCAA 57.279 33.333 23.14 0.00 40.14 2.69
4558 4599 6.045072 TCGATACTTATTCAACCACAACCT 57.955 37.500 0.00 0.00 0.00 3.50
4574 4615 5.057149 CACAACCTGGCTGTTATATAGGTC 58.943 45.833 0.00 0.00 40.70 3.85
4594 4635 6.296803 AGGTCCAACTTTAACTTAAGGTGAG 58.703 40.000 2.38 3.78 43.93 3.51
4616 4657 6.144078 AGAGTAACGAAAATTGCTTTTGGT 57.856 33.333 0.00 0.00 42.75 3.67
4621 4662 2.570135 GAAAATTGCTTTTGGTGGCCA 58.430 42.857 0.00 0.00 34.73 5.36
4631 4672 2.036256 GGTGGCCAAGCTCCATGT 59.964 61.111 7.24 0.00 35.81 3.21
4646 4687 4.456566 GCTCCATGTAGGTCGGTTTTTAAA 59.543 41.667 0.00 0.00 39.02 1.52
4649 4690 6.972722 TCCATGTAGGTCGGTTTTTAAAAAG 58.027 36.000 13.58 3.84 39.02 2.27
4712 4818 5.330455 ACATACAGATATACATGGAGGCG 57.670 43.478 0.00 0.00 0.00 5.52
4716 4822 5.801531 ACAGATATACATGGAGGCGTAAA 57.198 39.130 0.00 0.00 0.00 2.01
4762 4868 6.041296 AGGATGAAATACATTGAAATGAGGGC 59.959 38.462 9.94 0.00 39.56 5.19
4764 4870 7.231317 GGATGAAATACATTGAAATGAGGGCTA 59.769 37.037 9.94 0.00 39.56 3.93
4768 4874 3.634504 ACATTGAAATGAGGGCTATGCA 58.365 40.909 9.94 0.00 39.67 3.96
4769 4875 4.025360 ACATTGAAATGAGGGCTATGCAA 58.975 39.130 9.94 0.00 39.67 4.08
4770 4876 4.467082 ACATTGAAATGAGGGCTATGCAAA 59.533 37.500 9.94 0.00 39.67 3.68
4813 4950 3.098377 CACATGATTGTTCATCCCCCAA 58.902 45.455 0.00 0.00 40.70 4.12
4839 4977 5.066375 TCGCATTTCAAGGTATTTCATCCTG 59.934 40.000 0.00 0.00 33.97 3.86
4871 5010 3.691118 ACACATACACATCACATCCTTGC 59.309 43.478 0.00 0.00 0.00 4.01
4882 5021 4.180817 TCACATCCTTGCATACTTGTACG 58.819 43.478 0.00 0.00 0.00 3.67
4884 5023 4.032900 CACATCCTTGCATACTTGTACGAC 59.967 45.833 0.00 0.00 0.00 4.34
4963 5114 3.431725 CGAGCTCCAAAACGCCCC 61.432 66.667 8.47 0.00 0.00 5.80
4983 5135 5.178797 CCCCACTATAGTTCTTGTGTCTTG 58.821 45.833 1.56 0.00 0.00 3.02
5021 5173 2.450345 GCGAGGTTTAACCCGAGCG 61.450 63.158 22.43 16.50 39.75 5.03
5022 5174 2.450345 CGAGGTTTAACCCGAGCGC 61.450 63.158 10.93 0.00 39.75 5.92
5023 5175 1.079336 GAGGTTTAACCCGAGCGCT 60.079 57.895 11.27 11.27 39.75 5.92
5024 5176 1.359459 GAGGTTTAACCCGAGCGCTG 61.359 60.000 18.48 7.34 39.75 5.18
5025 5177 1.375013 GGTTTAACCCGAGCGCTGA 60.375 57.895 18.48 0.00 30.04 4.26
5026 5178 0.743345 GGTTTAACCCGAGCGCTGAT 60.743 55.000 18.48 0.00 30.04 2.90
5027 5179 0.373716 GTTTAACCCGAGCGCTGATG 59.626 55.000 18.48 4.61 0.00 3.07
5028 5180 0.742990 TTTAACCCGAGCGCTGATGG 60.743 55.000 18.48 15.20 0.00 3.51
5029 5181 3.733344 TAACCCGAGCGCTGATGGC 62.733 63.158 18.48 0.00 37.64 4.40
5032 5184 4.923942 CCGAGCGCTGATGGCCAT 62.924 66.667 20.96 20.96 37.74 4.40
5033 5185 3.344215 CGAGCGCTGATGGCCATC 61.344 66.667 34.71 34.71 37.74 3.51
5034 5186 2.976903 GAGCGCTGATGGCCATCC 60.977 66.667 36.97 23.94 37.02 3.51
5035 5187 4.923942 AGCGCTGATGGCCATCCG 62.924 66.667 36.97 32.80 37.02 4.18
5036 5188 4.916293 GCGCTGATGGCCATCCGA 62.916 66.667 36.97 22.01 37.02 4.55
5037 5189 2.031616 CGCTGATGGCCATCCGAT 59.968 61.111 36.97 9.70 37.02 4.18
5038 5190 1.598962 CGCTGATGGCCATCCGATT 60.599 57.895 36.97 8.85 37.02 3.34
5039 5191 1.572085 CGCTGATGGCCATCCGATTC 61.572 60.000 36.97 21.48 37.02 2.52
5040 5192 1.239968 GCTGATGGCCATCCGATTCC 61.240 60.000 36.97 17.66 37.02 3.01
5041 5193 0.109153 CTGATGGCCATCCGATTCCA 59.891 55.000 36.97 19.82 37.02 3.53
5042 5194 0.179020 TGATGGCCATCCGATTCCAC 60.179 55.000 36.97 14.90 37.02 4.02
5043 5195 0.179020 GATGGCCATCCGATTCCACA 60.179 55.000 32.15 0.00 34.14 4.17
5044 5196 0.258484 ATGGCCATCCGATTCCACAA 59.742 50.000 14.09 0.00 34.14 3.33
5045 5197 0.038890 TGGCCATCCGATTCCACAAA 59.961 50.000 0.00 0.00 34.14 2.83
5046 5198 0.455815 GGCCATCCGATTCCACAAAC 59.544 55.000 0.00 0.00 0.00 2.93
5047 5199 0.455815 GCCATCCGATTCCACAAACC 59.544 55.000 0.00 0.00 0.00 3.27
5048 5200 0.732571 CCATCCGATTCCACAAACCG 59.267 55.000 0.00 0.00 0.00 4.44
5049 5201 1.448985 CATCCGATTCCACAAACCGT 58.551 50.000 0.00 0.00 0.00 4.83
5050 5202 1.810151 CATCCGATTCCACAAACCGTT 59.190 47.619 0.00 0.00 0.00 4.44
5051 5203 1.970092 TCCGATTCCACAAACCGTTT 58.030 45.000 0.00 0.00 0.00 3.60
5052 5204 2.299521 TCCGATTCCACAAACCGTTTT 58.700 42.857 0.00 0.00 0.00 2.43
5053 5205 2.291190 TCCGATTCCACAAACCGTTTTC 59.709 45.455 0.00 0.00 0.00 2.29
5054 5206 2.033550 CCGATTCCACAAACCGTTTTCA 59.966 45.455 0.00 0.00 0.00 2.69
5055 5207 3.296628 CGATTCCACAAACCGTTTTCAG 58.703 45.455 0.00 0.00 0.00 3.02
5056 5208 3.002862 CGATTCCACAAACCGTTTTCAGA 59.997 43.478 0.00 0.00 0.00 3.27
5087 5271 3.004524 AGCTAACTGAAGAAACTCGACGT 59.995 43.478 0.00 0.00 0.00 4.34
5090 5274 5.276726 GCTAACTGAAGAAACTCGACGTTTT 60.277 40.000 12.25 0.00 45.48 2.43
5095 5281 1.937899 AGAAACTCGACGTTTTGTGGG 59.062 47.619 12.25 0.00 45.48 4.61
5183 5411 8.554528 GCATATAGCAGCCATATTACATAGTTG 58.445 37.037 0.00 0.00 44.79 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.880027 GAAAATCACCAACGAGCAGGT 59.120 47.619 0.00 0.00 39.10 4.00
155 156 2.293399 ACGACTTTTCCAGGCACAAATC 59.707 45.455 0.00 0.00 0.00 2.17
205 206 2.047844 CAGCTGGGTCACGACAGG 60.048 66.667 5.57 0.00 35.30 4.00
222 223 2.359230 GGATGGGCAGCGATAGGC 60.359 66.667 0.00 0.00 44.05 3.93
223 224 2.219875 AGGGATGGGCAGCGATAGG 61.220 63.158 0.00 0.00 0.00 2.57
224 225 1.004080 CAGGGATGGGCAGCGATAG 60.004 63.158 0.00 0.00 0.00 2.08
225 226 3.150949 CAGGGATGGGCAGCGATA 58.849 61.111 0.00 0.00 0.00 2.92
226 227 4.575973 GCAGGGATGGGCAGCGAT 62.576 66.667 0.00 0.00 0.00 4.58
254 255 4.814294 GTGCGGGTGGAGTAGCGG 62.814 72.222 0.00 0.00 0.00 5.52
273 274 3.651562 AAAAATACGGTCGATTCGCAG 57.348 42.857 10.34 0.51 0.00 5.18
300 301 4.058797 GGAAACGGTGTCAGTGGG 57.941 61.111 0.00 0.00 0.00 4.61
333 334 1.839747 TGCTTGGTGGACGGGTACT 60.840 57.895 0.00 0.00 0.00 2.73
334 335 1.670083 GTGCTTGGTGGACGGGTAC 60.670 63.158 0.00 0.00 0.00 3.34
335 336 2.745037 GTGCTTGGTGGACGGGTA 59.255 61.111 0.00 0.00 0.00 3.69
336 337 4.265056 GGTGCTTGGTGGACGGGT 62.265 66.667 0.00 0.00 37.93 5.28
344 345 4.740822 GATGGGCGGGTGCTTGGT 62.741 66.667 0.00 0.00 42.25 3.67
346 347 4.738998 TGGATGGGCGGGTGCTTG 62.739 66.667 0.00 0.00 42.25 4.01
347 348 4.740822 GTGGATGGGCGGGTGCTT 62.741 66.667 0.00 0.00 42.25 3.91
401 402 0.098200 GGAGCGGCGGAAAATACAAC 59.902 55.000 9.78 0.00 0.00 3.32
459 460 3.957535 GGATGAGCGGCGGCAATG 61.958 66.667 19.21 0.00 43.41 2.82
475 476 3.357079 GTGGCTTGGCAGTGACGG 61.357 66.667 0.00 0.00 0.00 4.79
494 495 4.531426 TGGGTGTGTGGGTTGGGC 62.531 66.667 0.00 0.00 0.00 5.36
495 496 2.520741 GTGGGTGTGTGGGTTGGG 60.521 66.667 0.00 0.00 0.00 4.12
503 504 4.250305 GAGCGGTGGTGGGTGTGT 62.250 66.667 0.00 0.00 0.00 3.72
522 523 1.153647 GGGGCAAAAGTTATGCGGC 60.154 57.895 0.00 0.00 44.75 6.53
528 529 1.228429 AGCTGCGGGGCAAAAGTTA 60.228 52.632 0.00 0.00 38.41 2.24
714 721 7.295201 CAACAGAAAATGCAAATTTGGAGATG 58.705 34.615 19.47 13.44 30.13 2.90
731 738 6.434028 CCCTCTAAAATCATGTCCAACAGAAA 59.566 38.462 0.00 0.00 0.00 2.52
734 741 4.641989 CCCCTCTAAAATCATGTCCAACAG 59.358 45.833 0.00 0.00 0.00 3.16
758 765 2.209690 ACCGGACTGGGTAAATTTGG 57.790 50.000 9.46 0.00 44.64 3.28
759 766 3.570550 TGAAACCGGACTGGGTAAATTTG 59.429 43.478 9.46 0.00 35.58 2.32
851 861 1.599419 GGTGCGTCATTTTGGTGACAC 60.599 52.381 7.67 0.00 46.89 3.67
1093 1108 4.598894 CGGCTGCTGGATCTCCGG 62.599 72.222 0.00 0.00 45.30 5.14
1151 1166 2.750637 ATCTCGCCGTCGACCTGT 60.751 61.111 10.58 0.00 40.21 4.00
1330 1345 1.227380 CCATAGTCTGAGCACGGGC 60.227 63.158 0.00 0.00 41.61 6.13
1511 1526 1.226746 CCGTCTTCAACACCAAGACC 58.773 55.000 6.93 0.00 44.78 3.85
1518 1533 2.076863 AGCAATAGCCGTCTTCAACAC 58.923 47.619 0.00 0.00 43.56 3.32
1520 1535 2.076863 ACAGCAATAGCCGTCTTCAAC 58.923 47.619 0.00 0.00 43.56 3.18
1522 1537 2.346803 GAACAGCAATAGCCGTCTTCA 58.653 47.619 0.00 0.00 43.56 3.02
1526 1541 2.159085 AGTAGGAACAGCAATAGCCGTC 60.159 50.000 0.00 0.00 43.56 4.79
1529 1544 3.873910 TCAAGTAGGAACAGCAATAGCC 58.126 45.455 0.00 0.00 43.56 3.93
1532 1547 4.551702 TGCTCAAGTAGGAACAGCAATA 57.448 40.909 0.00 0.00 37.16 1.90
1535 1550 2.703416 CATGCTCAAGTAGGAACAGCA 58.297 47.619 0.00 0.00 43.96 4.41
1596 1619 4.828072 ACATTCTCCAGGTAAAGAGACC 57.172 45.455 0.00 0.00 38.83 3.85
1597 1620 5.187186 TGGTACATTCTCCAGGTAAAGAGAC 59.813 44.000 0.00 0.00 38.83 3.36
2032 2056 4.065321 AGAGCACATCTATTAGCACCAC 57.935 45.455 0.00 0.00 36.10 4.16
2206 2230 4.957759 ACACCACTGTAGTGTCAAAAAC 57.042 40.909 6.18 0.00 45.13 2.43
2219 2243 0.307760 GAGCGGTTTTGACACCACTG 59.692 55.000 0.00 0.00 36.49 3.66
2220 2244 0.180406 AGAGCGGTTTTGACACCACT 59.820 50.000 0.00 0.00 36.49 4.00
2221 2245 1.021968 AAGAGCGGTTTTGACACCAC 58.978 50.000 0.00 0.00 36.49 4.16
2222 2246 2.623878 TAAGAGCGGTTTTGACACCA 57.376 45.000 0.00 0.00 36.49 4.17
2223 2247 5.813080 AATATAAGAGCGGTTTTGACACC 57.187 39.130 0.00 0.00 0.00 4.16
2224 2248 7.352739 CCATAATATAAGAGCGGTTTTGACAC 58.647 38.462 0.00 0.00 0.00 3.67
2225 2249 6.485313 CCCATAATATAAGAGCGGTTTTGACA 59.515 38.462 0.00 0.00 0.00 3.58
2226 2250 6.708949 TCCCATAATATAAGAGCGGTTTTGAC 59.291 38.462 0.00 0.00 0.00 3.18
2227 2251 6.708949 GTCCCATAATATAAGAGCGGTTTTGA 59.291 38.462 0.00 0.00 0.00 2.69
2228 2252 6.347402 CGTCCCATAATATAAGAGCGGTTTTG 60.347 42.308 0.00 0.00 0.00 2.44
2229 2253 5.699458 CGTCCCATAATATAAGAGCGGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2230 2254 5.221581 ACGTCCCATAATATAAGAGCGGTTT 60.222 40.000 0.00 0.00 0.00 3.27
2231 2255 4.282703 ACGTCCCATAATATAAGAGCGGTT 59.717 41.667 0.00 0.00 0.00 4.44
2232 2256 3.830755 ACGTCCCATAATATAAGAGCGGT 59.169 43.478 0.00 0.00 0.00 5.68
2233 2257 4.451629 ACGTCCCATAATATAAGAGCGG 57.548 45.455 0.00 0.00 0.00 5.52
2234 2258 5.450137 CCCTACGTCCCATAATATAAGAGCG 60.450 48.000 0.00 0.00 0.00 5.03
2355 2379 9.033711 TCCATTTGTTTCATTCCAGAATCAATA 57.966 29.630 0.00 0.00 37.18 1.90
2463 2487 7.663827 TCATTCCGACTCTTCTGTAAAAGTAA 58.336 34.615 0.00 0.00 0.00 2.24
2466 2490 7.360438 CCTTTCATTCCGACTCTTCTGTAAAAG 60.360 40.741 0.00 0.00 0.00 2.27
2478 2502 6.940298 TCTGTAAATTTCCTTTCATTCCGACT 59.060 34.615 0.00 0.00 0.00 4.18
2652 2676 2.024414 CTTAGGCATTAAAAGGGCGCT 58.976 47.619 7.64 0.00 40.43 5.92
2811 2838 2.650322 TCTGGTTTTGCGGTTTTCTCT 58.350 42.857 0.00 0.00 0.00 3.10
2932 2963 8.082242 GCTGAACTTCAAACCACAACTTATAAT 58.918 33.333 0.00 0.00 0.00 1.28
3087 3118 5.242393 ACCAATCTCTTTCACCATTTGACTG 59.758 40.000 0.00 0.00 32.26 3.51
3315 3346 7.064728 CACAGCCTCTAAAACAACTAATCCTAC 59.935 40.741 0.00 0.00 0.00 3.18
3388 3419 6.935240 TTTCCATTCTCTAGAGGAACTTGA 57.065 37.500 19.67 6.70 41.55 3.02
3500 3531 4.875536 GTGCACAAAATTTCATTATCCCCC 59.124 41.667 13.17 0.00 0.00 5.40
3516 3547 1.031235 CCACCACTGAATGTGCACAA 58.969 50.000 25.72 6.58 44.92 3.33
3704 3735 4.148128 AGATAGGTGCAGGAGTCATTTG 57.852 45.455 0.00 0.00 0.00 2.32
3746 3777 5.429762 TGTCATGGGACTCTTTATCTCCAAT 59.570 40.000 0.00 0.00 44.61 3.16
3760 3791 1.369091 GATGGCACGTGTCATGGGAC 61.369 60.000 38.09 20.72 40.99 4.46
3828 3859 9.495572 AGGAAAACAAGTGTTGTAAAATCAAAA 57.504 25.926 0.00 0.00 44.59 2.44
3830 3861 9.575783 GTAGGAAAACAAGTGTTGTAAAATCAA 57.424 29.630 0.00 0.00 44.59 2.57
3832 3863 9.797556 AAGTAGGAAAACAAGTGTTGTAAAATC 57.202 29.630 0.00 0.00 44.59 2.17
3833 3864 9.581099 CAAGTAGGAAAACAAGTGTTGTAAAAT 57.419 29.630 0.00 0.00 44.59 1.82
3835 3866 7.030768 GCAAGTAGGAAAACAAGTGTTGTAAA 58.969 34.615 0.00 0.00 44.59 2.01
3836 3867 6.151312 TGCAAGTAGGAAAACAAGTGTTGTAA 59.849 34.615 0.00 0.00 44.59 2.41
3837 3868 5.648526 TGCAAGTAGGAAAACAAGTGTTGTA 59.351 36.000 0.00 0.00 44.59 2.41
3839 3870 4.992688 TGCAAGTAGGAAAACAAGTGTTG 58.007 39.130 0.00 0.00 38.44 3.33
3840 3871 5.652994 TTGCAAGTAGGAAAACAAGTGTT 57.347 34.783 0.00 0.00 40.50 3.32
3884 3915 1.141881 CGGGTTGACGATCTGGGAG 59.858 63.158 0.00 0.00 35.47 4.30
3885 3916 3.014085 GCGGGTTGACGATCTGGGA 62.014 63.158 0.00 0.00 35.47 4.37
3886 3917 2.511600 GCGGGTTGACGATCTGGG 60.512 66.667 0.00 0.00 35.47 4.45
3971 4003 6.517529 GCATTCTGAAAGGATCTACGGATAGT 60.518 42.308 0.00 0.00 19.36 2.12
4009 4041 0.933097 CGGCATGAGACTTCCATTCG 59.067 55.000 0.00 0.00 0.00 3.34
4023 4055 2.581354 GAGAGACCTGCACGGCAT 59.419 61.111 0.00 0.00 38.13 4.40
4052 4084 4.695217 ACAGTTGACATCGTGTGTTTTT 57.305 36.364 0.00 0.00 42.36 1.94
4076 4108 4.605640 AATGTACAAGCAAGCACCAATT 57.394 36.364 0.00 0.00 0.00 2.32
4189 4221 4.692155 CCAAGAAAGCCAGGCAATTTAAAG 59.308 41.667 15.80 0.00 0.00 1.85
4227 4259 1.043816 ACTCTCACTGGTCACCACTG 58.956 55.000 0.00 0.00 0.00 3.66
4255 4287 5.497474 AGGAAGGTATACGAGCAAACATTT 58.503 37.500 0.00 0.00 0.00 2.32
4291 4323 8.781196 ACATTCACATGCTCATAATGAATAGAC 58.219 33.333 15.41 0.00 35.64 2.59
4337 4369 6.486320 TGAATTACTGAAACATGCTCACAAGA 59.514 34.615 0.00 0.00 0.00 3.02
4354 4386 6.091713 GCATTTCAGCAGCAAAATGAATTACT 59.908 34.615 25.94 1.46 42.71 2.24
4380 4412 3.423539 CCAGAACTGGGATCTGACAAA 57.576 47.619 12.54 0.00 45.74 2.83
4422 4454 5.220605 CCCGATTTCTTCTTCGATTTACACC 60.221 44.000 0.00 0.00 37.55 4.16
4443 4475 0.109342 ATTCAGCCAGCTTATCCCCG 59.891 55.000 0.00 0.00 0.00 5.73
4458 4490 3.499338 ACAAATCTGGCACCTTGATTCA 58.501 40.909 0.82 0.00 31.03 2.57
4499 4534 9.716556 CCCAATACCTAGACCTAGAACATATAT 57.283 37.037 5.67 0.00 35.21 0.86
4521 4556 9.720769 GAATAAGTATCGAGAATTATTCCCCAA 57.279 33.333 29.09 0.56 38.10 4.12
4522 4557 8.876181 TGAATAAGTATCGAGAATTATTCCCCA 58.124 33.333 32.77 21.21 41.05 4.96
4558 4599 5.968676 AAGTTGGACCTATATAACAGCCA 57.031 39.130 0.00 0.00 0.00 4.75
4574 4615 8.771766 GTTACTCTCACCTTAAGTTAAAGTTGG 58.228 37.037 0.97 0.00 0.00 3.77
4594 4635 5.174943 CCACCAAAAGCAATTTTCGTTACTC 59.825 40.000 0.00 0.00 0.00 2.59
4616 4657 1.207488 ACCTACATGGAGCTTGGCCA 61.207 55.000 0.00 0.00 40.24 5.36
4621 4662 1.276622 AACCGACCTACATGGAGCTT 58.723 50.000 0.00 0.00 39.71 3.74
4631 4672 9.872721 ATTTTGAACTTTTTAAAAACCGACCTA 57.127 25.926 9.31 0.00 0.00 3.08
4741 4847 7.470424 GCATAGCCCTCATTTCAATGTATTTCA 60.470 37.037 0.00 0.00 37.65 2.69
4748 4854 4.659111 TTGCATAGCCCTCATTTCAATG 57.341 40.909 0.00 0.00 37.75 2.82
4749 4855 5.680594 TTTTGCATAGCCCTCATTTCAAT 57.319 34.783 0.00 0.00 0.00 2.57
4785 4894 3.557577 TGAACAATCATGTGCCGAAAG 57.442 42.857 0.00 0.00 40.46 2.62
4813 4950 6.322201 AGGATGAAATACCTTGAAATGCGATT 59.678 34.615 0.00 0.00 31.95 3.34
4839 4977 9.624697 ATGTGATGTGTATGTGTGTAAAATTTC 57.375 29.630 0.00 0.00 0.00 2.17
4843 4981 6.939730 AGGATGTGATGTGTATGTGTGTAAAA 59.060 34.615 0.00 0.00 0.00 1.52
4949 5100 0.679960 ATAGTGGGGCGTTTTGGAGC 60.680 55.000 0.00 0.00 0.00 4.70
4954 5105 3.994931 AGAACTATAGTGGGGCGTTTT 57.005 42.857 6.06 0.00 0.00 2.43
4963 5114 6.159293 TGCTCAAGACACAAGAACTATAGTG 58.841 40.000 6.06 0.00 37.95 2.74
4983 5135 0.458543 TCGACGGCTTGAGATTGCTC 60.459 55.000 0.00 0.00 41.67 4.26
5021 5173 1.239968 GGAATCGGATGGCCATCAGC 61.240 60.000 39.50 25.51 39.54 4.26
5022 5174 0.109153 TGGAATCGGATGGCCATCAG 59.891 55.000 39.50 36.15 39.54 2.90
5023 5175 0.179020 GTGGAATCGGATGGCCATCA 60.179 55.000 39.50 25.17 39.54 3.07
5024 5176 0.179020 TGTGGAATCGGATGGCCATC 60.179 55.000 33.90 33.90 37.11 3.51
5025 5177 0.258484 TTGTGGAATCGGATGGCCAT 59.742 50.000 20.96 20.96 32.26 4.40
5026 5178 0.038890 TTTGTGGAATCGGATGGCCA 59.961 50.000 8.56 8.56 0.00 5.36
5027 5179 0.455815 GTTTGTGGAATCGGATGGCC 59.544 55.000 0.00 0.00 0.00 5.36
5028 5180 0.455815 GGTTTGTGGAATCGGATGGC 59.544 55.000 0.00 0.00 0.00 4.40
5029 5181 0.732571 CGGTTTGTGGAATCGGATGG 59.267 55.000 0.00 0.00 38.20 3.51
5030 5182 1.448985 ACGGTTTGTGGAATCGGATG 58.551 50.000 0.00 0.00 46.06 3.51
5031 5183 2.194201 AACGGTTTGTGGAATCGGAT 57.806 45.000 0.00 0.00 46.06 4.18
5032 5184 1.970092 AAACGGTTTGTGGAATCGGA 58.030 45.000 5.12 0.00 46.06 4.55
5033 5185 2.033550 TGAAAACGGTTTGTGGAATCGG 59.966 45.455 1.45 0.00 46.06 4.18
5035 5187 4.561735 TCTGAAAACGGTTTGTGGAATC 57.438 40.909 1.45 0.54 0.00 2.52
5036 5188 4.401202 AGTTCTGAAAACGGTTTGTGGAAT 59.599 37.500 1.45 0.00 0.00 3.01
5037 5189 3.759618 AGTTCTGAAAACGGTTTGTGGAA 59.240 39.130 1.45 8.64 0.00 3.53
5038 5190 3.127895 CAGTTCTGAAAACGGTTTGTGGA 59.872 43.478 1.45 3.15 0.00 4.02
5039 5191 3.127895 TCAGTTCTGAAAACGGTTTGTGG 59.872 43.478 1.45 0.84 0.00 4.17
5040 5192 4.349663 TCAGTTCTGAAAACGGTTTGTG 57.650 40.909 1.45 0.00 0.00 3.33
5041 5193 5.587043 TGTATCAGTTCTGAAAACGGTTTGT 59.413 36.000 1.45 0.00 0.00 2.83
5042 5194 6.055231 TGTATCAGTTCTGAAAACGGTTTG 57.945 37.500 1.45 0.00 0.00 2.93
5043 5195 5.277828 GCTGTATCAGTTCTGAAAACGGTTT 60.278 40.000 19.23 0.00 33.43 3.27
5044 5196 4.213482 GCTGTATCAGTTCTGAAAACGGTT 59.787 41.667 19.23 0.00 33.43 4.44
5045 5197 3.746492 GCTGTATCAGTTCTGAAAACGGT 59.254 43.478 19.23 4.09 33.43 4.83
5046 5198 3.997021 AGCTGTATCAGTTCTGAAAACGG 59.003 43.478 16.38 16.38 33.43 4.44
5047 5199 6.366332 AGTTAGCTGTATCAGTTCTGAAAACG 59.634 38.462 6.60 6.45 33.43 3.60
5048 5200 7.385205 TCAGTTAGCTGTATCAGTTCTGAAAAC 59.615 37.037 6.47 8.64 43.05 2.43
5049 5201 7.441836 TCAGTTAGCTGTATCAGTTCTGAAAA 58.558 34.615 6.47 0.00 43.05 2.29
5050 5202 6.993079 TCAGTTAGCTGTATCAGTTCTGAAA 58.007 36.000 6.47 0.00 43.05 2.69
5051 5203 6.590234 TCAGTTAGCTGTATCAGTTCTGAA 57.410 37.500 6.47 0.00 43.05 3.02
5052 5204 6.434340 TCTTCAGTTAGCTGTATCAGTTCTGA 59.566 38.462 6.47 4.96 43.05 3.27
5053 5205 6.625362 TCTTCAGTTAGCTGTATCAGTTCTG 58.375 40.000 6.47 0.00 43.05 3.02
5054 5206 6.842437 TCTTCAGTTAGCTGTATCAGTTCT 57.158 37.500 6.47 0.00 43.05 3.01
5055 5207 7.600752 AGTTTCTTCAGTTAGCTGTATCAGTTC 59.399 37.037 6.47 0.00 43.05 3.01
5056 5208 7.445945 AGTTTCTTCAGTTAGCTGTATCAGTT 58.554 34.615 6.47 0.00 43.05 3.16
5234 5462 1.195115 GTGGTGGGCACTAGAGATCA 58.805 55.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.