Multiple sequence alignment - TraesCS2B01G568800

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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 TraesCS2B01G568800 chr2B 100.000 4599 0 0 1 4599 759489609 759494207 0.000000e+00 8493.0
1 TraesCS2B01G568800 chr2B 80.962 1040 167 23 2379 3391 708987022 708985987 0.000000e+00 795.0
2 TraesCS2B01G568800 chr2B 75.617 324 52 15 977 1283 708988020 708987707 8.030000e-28 135.0
3 TraesCS2B01G568800 chr2B 94.340 53 3 0 3616 3668 759493081 759493133 1.060000e-11 82.4
4 TraesCS2B01G568800 chr2B 94.340 53 3 0 3473 3525 759493224 759493276 1.060000e-11 82.4
5 TraesCS2B01G568800 chr2A 92.355 4395 241 52 41 4387 751418780 751423127 0.000000e+00 6167.0
6 TraesCS2B01G568800 chr2A 81.136 1039 167 15 2379 3391 721989664 721988629 0.000000e+00 806.0
7 TraesCS2B01G568800 chr2D 92.145 3590 220 31 34 3595 619731208 619734763 0.000000e+00 5011.0
8 TraesCS2B01G568800 chr2D 81.615 1028 161 13 2378 3378 587166873 587165847 0.000000e+00 826.0
9 TraesCS2B01G568800 chr2D 82.701 896 85 46 3542 4385 619734641 619735518 0.000000e+00 732.0
10 TraesCS2B01G568800 chr2D 77.561 205 34 6 1088 1283 587168227 587168026 3.760000e-21 113.0
11 TraesCS2B01G568800 chr2D 94.340 53 3 0 3616 3668 619734642 619734694 1.060000e-11 82.4
12 TraesCS2B01G568800 chr6B 85.876 177 13 5 4390 4563 101223421 101223254 1.310000e-40 178.0
13 TraesCS2B01G568800 chr5D 85.311 177 16 4 4394 4566 515337485 515337655 1.700000e-39 174.0
14 TraesCS2B01G568800 chr5D 81.281 203 22 8 4386 4580 550513215 550513409 2.870000e-32 150.0
15 TraesCS2B01G568800 chr7D 84.865 185 13 7 4394 4571 54659460 54659636 6.120000e-39 172.0
16 TraesCS2B01G568800 chr3D 84.066 182 16 5 4390 4565 51673539 51673713 3.680000e-36 163.0
17 TraesCS2B01G568800 chr3D 84.066 182 16 9 4394 4568 597833911 597833736 3.680000e-36 163.0
18 TraesCS2B01G568800 chr1A 88.028 142 12 5 4430 4570 307062844 307062981 3.680000e-36 163.0
19 TraesCS2B01G568800 chr4B 87.162 148 12 4 4424 4565 72741603 72741457 1.320000e-35 161.0
20 TraesCS2B01G568800 chr4A 85.256 156 19 3 4419 4573 605648334 605648182 1.710000e-34 158.0
21 TraesCS2B01G568800 chr5A 83.616 177 16 8 4396 4566 365601432 365601601 2.220000e-33 154.0
22 TraesCS2B01G568800 chr5A 81.143 175 25 3 4394 4566 660882913 660883081 2.890000e-27 134.0


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 TraesCS2B01G568800 chr2B 759489609 759494207 4598 False 2885.933333 8493 96.226667 1 4599 3 chr2B.!!$F1 4598
1 TraesCS2B01G568800 chr2B 708985987 708988020 2033 True 465.000000 795 78.289500 977 3391 2 chr2B.!!$R1 2414
2 TraesCS2B01G568800 chr2A 751418780 751423127 4347 False 6167.000000 6167 92.355000 41 4387 1 chr2A.!!$F1 4346
3 TraesCS2B01G568800 chr2A 721988629 721989664 1035 True 806.000000 806 81.136000 2379 3391 1 chr2A.!!$R1 1012
4 TraesCS2B01G568800 chr2D 619731208 619735518 4310 False 1941.800000 5011 89.728667 34 4385 3 chr2D.!!$F1 4351
5 TraesCS2B01G568800 chr2D 587165847 587168227 2380 True 469.500000 826 79.588000 1088 3378 2 chr2D.!!$R1 2290

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
813 825 0.104934 AGCTTCCCCTGGACCGATAT 60.105 55.0 0.00 0.0 0.00 1.63 F
1196 1226 1.352622 ACCTCAACCTTGACCCAGCA 61.353 55.0 0.00 0.0 32.90 4.41 F
2182 2233 0.523072 ACATAGCAAGGCAGCAAACG 59.477 50.0 4.78 0.0 36.85 3.60 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 1716 1.017387 CAGTTTTCGCCTATCCCTGC 58.983 55.0 0.0 0.0 0.0 4.85 R
2835 3452 0.696501 GGCCACCCTCCTTACTTCAA 59.303 55.0 0.0 0.0 0.0 2.69 R
3818 4477 0.546122 TATGCCCGACCTTGCTGATT 59.454 50.0 0.0 0.0 0.0 2.57 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
17 18 3.432186 ACCAGCAGCGAAAACCAC 58.568 55.556 0.00 0.00 0.00 4.16
18 19 1.152963 ACCAGCAGCGAAAACCACT 60.153 52.632 0.00 0.00 0.00 4.00
19 20 0.751643 ACCAGCAGCGAAAACCACTT 60.752 50.000 0.00 0.00 0.00 3.16
20 21 0.318107 CCAGCAGCGAAAACCACTTG 60.318 55.000 0.00 0.00 0.00 3.16
21 22 0.936297 CAGCAGCGAAAACCACTTGC 60.936 55.000 0.00 0.00 0.00 4.01
22 23 1.661509 GCAGCGAAAACCACTTGCC 60.662 57.895 0.00 0.00 0.00 4.52
23 24 2.032981 CAGCGAAAACCACTTGCCT 58.967 52.632 0.00 0.00 0.00 4.75
24 25 0.385390 CAGCGAAAACCACTTGCCTT 59.615 50.000 0.00 0.00 0.00 4.35
25 26 0.668535 AGCGAAAACCACTTGCCTTC 59.331 50.000 0.00 0.00 0.00 3.46
26 27 0.383949 GCGAAAACCACTTGCCTTCA 59.616 50.000 0.00 0.00 0.00 3.02
27 28 1.000274 GCGAAAACCACTTGCCTTCAT 60.000 47.619 0.00 0.00 0.00 2.57
28 29 2.922335 GCGAAAACCACTTGCCTTCATC 60.922 50.000 0.00 0.00 0.00 2.92
29 30 2.293122 CGAAAACCACTTGCCTTCATCA 59.707 45.455 0.00 0.00 0.00 3.07
30 31 3.057315 CGAAAACCACTTGCCTTCATCAT 60.057 43.478 0.00 0.00 0.00 2.45
31 32 4.559300 CGAAAACCACTTGCCTTCATCATT 60.559 41.667 0.00 0.00 0.00 2.57
32 33 4.525912 AAACCACTTGCCTTCATCATTC 57.474 40.909 0.00 0.00 0.00 2.67
36 37 3.028850 CACTTGCCTTCATCATTCCCAT 58.971 45.455 0.00 0.00 0.00 4.00
39 40 4.161001 ACTTGCCTTCATCATTCCCATTTC 59.839 41.667 0.00 0.00 0.00 2.17
42 43 2.624838 CCTTCATCATTCCCATTTCCCG 59.375 50.000 0.00 0.00 0.00 5.14
57 58 0.821517 TCCCGTACAACATCATCGCT 59.178 50.000 0.00 0.00 0.00 4.93
59 60 1.640428 CCGTACAACATCATCGCTGT 58.360 50.000 0.00 0.00 0.00 4.40
90 91 4.802051 ATCCCAGTTGCGCCGCAT 62.802 61.111 14.63 0.00 38.76 4.73
136 137 2.105128 GGACATGAGAGGCGTCGG 59.895 66.667 0.00 0.00 0.00 4.79
137 138 2.711922 GGACATGAGAGGCGTCGGT 61.712 63.158 0.00 0.00 0.00 4.69
138 139 1.226717 GACATGAGAGGCGTCGGTC 60.227 63.158 0.00 4.59 0.00 4.79
139 140 2.278206 CATGAGAGGCGTCGGTCG 60.278 66.667 0.00 0.00 43.12 4.79
171 172 5.957220 GCAACCGACAAAATTGAACTTTTTC 59.043 36.000 0.00 0.00 0.00 2.29
175 176 5.038033 CGACAAAATTGAACTTTTTCGGGA 58.962 37.500 0.37 0.00 34.04 5.14
176 177 5.051973 CGACAAAATTGAACTTTTTCGGGAC 60.052 40.000 0.37 0.00 34.04 4.46
179 180 2.740506 TTGAACTTTTTCGGGACCCT 57.259 45.000 9.41 0.00 34.04 4.34
180 181 1.975660 TGAACTTTTTCGGGACCCTG 58.024 50.000 9.41 2.25 34.04 4.45
181 182 1.491332 TGAACTTTTTCGGGACCCTGA 59.509 47.619 9.41 4.91 34.04 3.86
182 183 2.107552 TGAACTTTTTCGGGACCCTGAT 59.892 45.455 9.41 0.00 34.04 2.90
183 184 3.328343 TGAACTTTTTCGGGACCCTGATA 59.672 43.478 9.41 0.32 34.04 2.15
184 185 3.345508 ACTTTTTCGGGACCCTGATAC 57.654 47.619 9.41 0.00 0.00 2.24
185 186 2.910977 ACTTTTTCGGGACCCTGATACT 59.089 45.455 9.41 0.00 0.00 2.12
186 187 3.270877 CTTTTTCGGGACCCTGATACTG 58.729 50.000 9.41 0.00 0.00 2.74
187 188 0.539986 TTTCGGGACCCTGATACTGC 59.460 55.000 9.41 0.00 0.00 4.40
188 189 1.672854 TTCGGGACCCTGATACTGCG 61.673 60.000 9.41 0.00 0.00 5.18
189 190 2.109181 GGGACCCTGATACTGCGC 59.891 66.667 2.09 0.00 0.00 6.09
193 194 2.109799 CCCTGATACTGCGCCCAG 59.890 66.667 4.18 0.00 44.80 4.45
202 203 1.002624 CTGCGCCCAGAGGGTTTTA 60.003 57.895 4.18 0.00 46.51 1.52
203 204 0.608035 CTGCGCCCAGAGGGTTTTAA 60.608 55.000 4.18 0.00 46.51 1.52
204 205 0.891904 TGCGCCCAGAGGGTTTTAAC 60.892 55.000 4.18 0.00 46.51 2.01
205 206 0.608308 GCGCCCAGAGGGTTTTAACT 60.608 55.000 0.00 0.00 46.51 2.24
206 207 1.339342 GCGCCCAGAGGGTTTTAACTA 60.339 52.381 0.00 0.00 46.51 2.24
244 245 2.506472 GTCCGGGATTCCAGCCTC 59.494 66.667 0.00 0.00 0.00 4.70
264 265 3.586174 CTCCATGATCACCCACTGGATAT 59.414 47.826 13.98 0.00 35.55 1.63
271 272 0.839946 ACCCACTGGATATGACAGCC 59.160 55.000 0.00 0.00 39.55 4.85
275 276 1.363807 CTGGATATGACAGCCGCGA 59.636 57.895 8.23 0.00 34.41 5.87
276 277 0.249447 CTGGATATGACAGCCGCGAA 60.249 55.000 8.23 0.00 34.41 4.70
277 278 0.176910 TGGATATGACAGCCGCGAAA 59.823 50.000 8.23 0.00 34.41 3.46
301 302 4.486125 AAAATGGGCAGAAACAAGTTGT 57.514 36.364 1.64 1.64 0.00 3.32
377 382 7.553044 GCATAACAGGAACAAAGAAGTATAGGT 59.447 37.037 0.00 0.00 0.00 3.08
378 383 9.099454 CATAACAGGAACAAAGAAGTATAGGTC 57.901 37.037 0.00 0.00 0.00 3.85
394 399 0.108520 GGTCGCATGGAACGTAGGAA 60.109 55.000 0.00 0.00 0.00 3.36
413 418 7.931948 CGTAGGAATAAGATACTCCCAATTTGT 59.068 37.037 0.00 0.00 0.00 2.83
444 450 2.014857 GGGATAGCCGAAGTTTCCAAC 58.985 52.381 0.00 0.00 33.83 3.77
521 531 2.358898 CAGAAACAAGTTGTGTCCCAGG 59.641 50.000 20.47 6.49 40.60 4.45
558 568 3.181495 TGCGTCCTAAACAAAAACCAGTG 60.181 43.478 0.00 0.00 0.00 3.66
577 587 1.207089 TGGCATACCAGGACGAAGAAG 59.793 52.381 0.00 0.00 42.67 2.85
578 588 1.207329 GGCATACCAGGACGAAGAAGT 59.793 52.381 0.00 0.00 35.26 3.01
708 720 4.863131 CGCGGTATTAAGATACTCCCAATC 59.137 45.833 0.00 0.00 38.53 2.67
739 751 2.030401 GCACACGGGCGACATGTAA 61.030 57.895 0.00 0.00 30.74 2.41
752 764 6.649141 GGGCGACATGTAAGAATATTCACATA 59.351 38.462 17.56 5.11 30.66 2.29
772 784 0.472471 TTGTCGGGCTCTTCCTGTTT 59.528 50.000 0.00 0.00 42.13 2.83
786 798 1.885163 CTGTTTCCGACGTAGGCCCT 61.885 60.000 10.23 0.00 0.00 5.19
813 825 0.104934 AGCTTCCCCTGGACCGATAT 60.105 55.000 0.00 0.00 0.00 1.63
909 923 3.513515 GTCCAAGTGAGAAGGATCAGACT 59.486 47.826 0.00 0.00 33.33 3.24
1170 1200 1.594194 GCCAATGCCGGTGATCAACA 61.594 55.000 12.13 1.49 0.00 3.33
1196 1226 1.352622 ACCTCAACCTTGACCCAGCA 61.353 55.000 0.00 0.00 32.90 4.41
1341 1371 5.574443 GCATTTATCTTTTCCAGACTGCAAC 59.426 40.000 0.00 0.00 32.83 4.17
1357 1387 1.469079 GCAACGGATAACATTGCCACC 60.469 52.381 0.00 0.00 42.32 4.61
1485 1517 7.503902 GGAAAATTAGGAGCTATGATGACCTTT 59.496 37.037 0.00 0.00 32.90 3.11
1486 1518 9.561069 GAAAATTAGGAGCTATGATGACCTTTA 57.439 33.333 0.00 0.00 32.90 1.85
1535 1567 6.270815 CACCGCATTGTTAGTAGTAGTACAT 58.729 40.000 10.33 0.00 0.00 2.29
1540 1572 6.533723 GCATTGTTAGTAGTAGTACATGCACA 59.466 38.462 18.27 9.65 31.50 4.57
1582 1616 5.163814 CCTGCACTCAGCTAAATAGTTTGAC 60.164 44.000 0.00 0.00 45.94 3.18
1619 1653 1.923356 TGTCCCCCAAAATGAAGAGC 58.077 50.000 0.00 0.00 0.00 4.09
1624 1658 2.833338 CCCCCAAAATGAAGAGCATGAA 59.167 45.455 0.00 0.00 37.28 2.57
1636 1670 5.764686 TGAAGAGCATGAACTGTGTAAACAT 59.235 36.000 0.00 0.00 0.00 2.71
1642 1677 7.530010 AGCATGAACTGTGTAAACATTGATAC 58.470 34.615 0.00 0.00 0.00 2.24
1681 1716 1.202452 TCATGCGACTGTATGAGGCAG 60.202 52.381 0.00 0.00 41.50 4.85
1689 1724 1.973515 CTGTATGAGGCAGCAGGGATA 59.026 52.381 0.00 0.00 0.00 2.59
1711 1746 2.663119 GGCGAAAACTGTACGATACGTT 59.337 45.455 0.00 0.00 41.54 3.99
1735 1770 1.130561 GACCAGCTACATTTTGTCGCC 59.869 52.381 1.08 0.00 39.55 5.54
1772 1807 6.492007 ACTGACAAATAACATGAAGCTGAG 57.508 37.500 0.00 0.00 0.00 3.35
1801 1845 3.054065 AGTCCCCATTTCATCCTTCAGTC 60.054 47.826 0.00 0.00 0.00 3.51
1808 1852 4.639078 TTTCATCCTTCAGTCATCACCA 57.361 40.909 0.00 0.00 0.00 4.17
1828 1872 4.101898 ACCACAATGACACCAGTACTACAA 59.898 41.667 0.00 0.00 0.00 2.41
1833 1877 6.995686 ACAATGACACCAGTACTACAATGAAA 59.004 34.615 0.00 0.00 0.00 2.69
1867 1913 5.581085 GCACTTGTCGGTTGTAGATAATTCT 59.419 40.000 0.00 0.00 35.90 2.40
1868 1914 6.092259 GCACTTGTCGGTTGTAGATAATTCTT 59.908 38.462 0.00 0.00 33.17 2.52
1925 1973 8.846943 TGATGTAACATTTCAGTATTGAGTGT 57.153 30.769 3.51 3.51 36.29 3.55
2148 2199 2.995466 AACAACTGCATCATTGTCCG 57.005 45.000 10.52 0.00 38.08 4.79
2182 2233 0.523072 ACATAGCAAGGCAGCAAACG 59.477 50.000 4.78 0.00 36.85 3.60
2198 2701 4.111916 GCAAACGGTATTACTAAGGCGTA 58.888 43.478 0.00 0.00 0.00 4.42
2673 3284 0.901580 GCATTATGCCCATCCCCTGG 60.902 60.000 5.80 0.00 45.51 4.45
2723 3334 2.534990 CCCCCAATCTACAGGCAAAAA 58.465 47.619 0.00 0.00 0.00 1.94
2817 3434 6.485313 TGTTCATGTACTAAAAACAGGGAGTG 59.515 38.462 4.01 0.00 29.93 3.51
2835 3452 5.598417 GGGAGTGTATGGGAAATTTTGCTAT 59.402 40.000 4.97 4.97 0.00 2.97
3148 3765 1.808945 CACATGGAAGTCCTGAGCAAC 59.191 52.381 0.00 0.00 36.82 4.17
3232 3849 1.802508 GCCAGCATTAATGGTTTCGCC 60.803 52.381 17.28 0.00 40.17 5.54
3251 3868 1.489649 CCATGCATGAGAAGGTCTCCT 59.510 52.381 28.31 0.00 42.73 3.69
3343 3960 5.021033 ACTATCTCACAAGCAATCTGGAG 57.979 43.478 0.00 0.00 0.00 3.86
3397 4014 3.103091 GCAAGGGGCGTAGTAGGGG 62.103 68.421 0.00 0.00 0.00 4.79
3424 4041 1.939934 CTCCACTCGAAGCACAAAACA 59.060 47.619 0.00 0.00 0.00 2.83
3437 4054 4.817464 AGCACAAAACAATACCTACGACAA 59.183 37.500 0.00 0.00 0.00 3.18
3575 4192 5.629849 CGATCTGAAAGTACTGAAGTCGTTT 59.370 40.000 0.00 0.00 33.76 3.60
3583 4200 4.933400 AGTACTGAAGTCGTTTTGTGTTGT 59.067 37.500 0.00 0.00 0.00 3.32
3591 4208 2.680339 TCGTTTTGTGTTGTCATGCTGA 59.320 40.909 0.00 0.00 0.00 4.26
3608 4225 9.241317 GTCATGCTGATTTGGACAAATTATTAG 57.759 33.333 11.20 8.89 40.77 1.73
3654 4272 2.094752 GGCACTGAAGTTGTTGTGTGTT 60.095 45.455 0.00 0.00 33.44 3.32
3655 4273 2.916716 GCACTGAAGTTGTTGTGTGTTG 59.083 45.455 0.00 0.00 33.44 3.33
3656 4274 3.611530 GCACTGAAGTTGTTGTGTGTTGT 60.612 43.478 0.00 0.00 33.44 3.32
3683 4302 0.105401 TTTTCCCCTTTCACCCCACC 60.105 55.000 0.00 0.00 0.00 4.61
3693 4312 5.208121 CCTTTCACCCCACCACATTATTAT 58.792 41.667 0.00 0.00 0.00 1.28
3743 4365 9.784531 ATCCATGATGTAAACTTTATCTACCTG 57.215 33.333 0.00 0.00 0.00 4.00
3744 4366 8.988060 TCCATGATGTAAACTTTATCTACCTGA 58.012 33.333 0.00 0.00 0.00 3.86
3745 4367 9.265901 CCATGATGTAAACTTTATCTACCTGAG 57.734 37.037 0.00 0.00 0.00 3.35
3746 4368 9.823647 CATGATGTAAACTTTATCTACCTGAGT 57.176 33.333 0.00 0.00 0.00 3.41
3770 4397 6.452494 AGTAGTAAGGTACTGTATGCTGTG 57.548 41.667 3.59 0.00 40.86 3.66
3776 4403 5.995565 AGGTACTGTATGCTGTGAGTTAA 57.004 39.130 3.59 0.00 37.18 2.01
3818 4477 3.431912 CACTTGTAATGCTGCGACACTTA 59.568 43.478 0.00 0.00 0.00 2.24
3830 4489 2.094417 GCGACACTTAATCAGCAAGGTC 59.906 50.000 0.00 0.00 0.00 3.85
3833 4492 2.009774 CACTTAATCAGCAAGGTCGGG 58.990 52.381 0.00 0.00 0.00 5.14
3876 4535 8.729805 AGAATCAGTAAGAACAAGATTGGATC 57.270 34.615 0.00 0.00 34.63 3.36
3879 4538 3.865745 AGTAAGAACAAGATTGGATCGCG 59.134 43.478 0.00 0.00 0.00 5.87
3899 4558 2.590092 GGTTCCTCCGTGGATGGG 59.410 66.667 0.00 0.00 45.68 4.00
3935 4594 1.696097 ATCGAAATGGAGGACGGGGG 61.696 60.000 0.00 0.00 0.00 5.40
3950 4609 0.624254 GGGGGTGGGGAAGAAACTAG 59.376 60.000 0.00 0.00 0.00 2.57
3968 4627 2.265589 AGTACCAAACAGAAACCCCG 57.734 50.000 0.00 0.00 0.00 5.73
3971 4630 1.152631 CCAAACAGAAACCCCGGGT 60.153 57.895 21.85 2.03 37.65 5.28
4082 4757 1.224592 GTAGTAGGTCCCGTCCCGA 59.775 63.158 0.00 0.00 0.00 5.14
4315 4999 2.034939 TCGTCCTACGCTCAAGTCAAAA 59.965 45.455 0.00 0.00 42.21 2.44
4316 5000 2.798283 CGTCCTACGCTCAAGTCAAAAA 59.202 45.455 0.00 0.00 33.65 1.94
4322 5006 2.827555 CGCTCAAGTCAAAAAGTAGCG 58.172 47.619 0.00 0.00 44.22 4.26
4324 5008 2.806244 GCTCAAGTCAAAAAGTAGCGGA 59.194 45.455 0.00 0.00 0.00 5.54
4333 5019 6.262273 AGTCAAAAAGTAGCGGATCAAAGAAA 59.738 34.615 0.00 0.00 0.00 2.52
4360 5046 7.818930 GTGGAAAATGCTTGGAGAAAATAATCA 59.181 33.333 0.00 0.00 0.00 2.57
4395 5081 4.911514 CTTCCTTTGAAGGTTTTTCGGA 57.088 40.909 9.48 0.00 46.54 4.55
4396 5082 4.607955 CTTCCTTTGAAGGTTTTTCGGAC 58.392 43.478 9.48 0.00 46.54 4.79
4397 5083 3.622630 TCCTTTGAAGGTTTTTCGGACA 58.377 40.909 9.48 0.00 46.54 4.02
4398 5084 3.379057 TCCTTTGAAGGTTTTTCGGACAC 59.621 43.478 9.48 0.00 46.54 3.67
4399 5085 3.129638 CCTTTGAAGGTTTTTCGGACACA 59.870 43.478 1.49 0.00 41.41 3.72
4400 5086 4.202111 CCTTTGAAGGTTTTTCGGACACAT 60.202 41.667 1.49 0.00 41.41 3.21
4401 5087 4.561735 TTGAAGGTTTTTCGGACACATC 57.438 40.909 0.00 0.00 0.00 3.06
4402 5088 3.815809 TGAAGGTTTTTCGGACACATCT 58.184 40.909 0.00 0.00 0.00 2.90
4403 5089 4.963373 TGAAGGTTTTTCGGACACATCTA 58.037 39.130 0.00 0.00 0.00 1.98
4404 5090 4.994852 TGAAGGTTTTTCGGACACATCTAG 59.005 41.667 0.00 0.00 0.00 2.43
4405 5091 4.884668 AGGTTTTTCGGACACATCTAGA 57.115 40.909 0.00 0.00 0.00 2.43
4406 5092 4.566987 AGGTTTTTCGGACACATCTAGAC 58.433 43.478 0.00 0.00 0.00 2.59
4407 5093 3.367025 GGTTTTTCGGACACATCTAGACG 59.633 47.826 0.00 0.00 0.00 4.18
4408 5094 3.928727 TTTTCGGACACATCTAGACGT 57.071 42.857 0.00 0.00 0.00 4.34
4409 5095 2.913777 TTCGGACACATCTAGACGTG 57.086 50.000 17.02 17.02 39.10 4.49
4410 5096 2.103537 TCGGACACATCTAGACGTGA 57.896 50.000 24.69 0.00 36.91 4.35
4411 5097 1.736126 TCGGACACATCTAGACGTGAC 59.264 52.381 24.69 18.11 36.91 3.67
4412 5098 1.467342 CGGACACATCTAGACGTGACA 59.533 52.381 24.69 0.00 36.91 3.58
4413 5099 2.097629 CGGACACATCTAGACGTGACAT 59.902 50.000 24.69 3.01 36.91 3.06
4414 5100 3.311596 CGGACACATCTAGACGTGACATA 59.688 47.826 24.69 0.00 36.91 2.29
4415 5101 4.552961 CGGACACATCTAGACGTGACATAG 60.553 50.000 24.69 10.31 36.91 2.23
4416 5102 4.335874 GGACACATCTAGACGTGACATAGT 59.664 45.833 24.69 1.47 36.91 2.12
4417 5103 5.163642 GGACACATCTAGACGTGACATAGTT 60.164 44.000 24.69 0.71 36.91 2.24
4418 5104 6.037940 GGACACATCTAGACGTGACATAGTTA 59.962 42.308 24.69 0.00 36.91 2.24
4419 5105 7.255173 GGACACATCTAGACGTGACATAGTTAT 60.255 40.741 24.69 0.00 36.91 1.89
4420 5106 7.418408 ACACATCTAGACGTGACATAGTTATG 58.582 38.462 24.69 2.46 36.89 1.90
4422 5108 8.557029 CACATCTAGACGTGACATAGTTATGTA 58.443 37.037 13.63 0.00 46.20 2.29
4423 5109 9.117183 ACATCTAGACGTGACATAGTTATGTAA 57.883 33.333 4.84 0.00 46.20 2.41
4452 5138 4.691175 CATCTAACCTGATGTCCACTCTG 58.309 47.826 0.00 0.00 39.05 3.35
4453 5139 3.779444 TCTAACCTGATGTCCACTCTGT 58.221 45.455 0.00 0.00 0.00 3.41
4454 5140 4.160329 TCTAACCTGATGTCCACTCTGTT 58.840 43.478 0.00 0.00 0.00 3.16
4455 5141 3.864789 AACCTGATGTCCACTCTGTTT 57.135 42.857 0.00 0.00 0.00 2.83
4456 5142 3.131709 ACCTGATGTCCACTCTGTTTG 57.868 47.619 0.00 0.00 0.00 2.93
4457 5143 2.439507 ACCTGATGTCCACTCTGTTTGT 59.560 45.455 0.00 0.00 0.00 2.83
4458 5144 2.810274 CCTGATGTCCACTCTGTTTGTG 59.190 50.000 0.00 0.00 35.39 3.33
4472 5158 8.967218 CACTCTGTTTGTGGTATAATTGTTTTG 58.033 33.333 0.00 0.00 0.00 2.44
4473 5159 8.691797 ACTCTGTTTGTGGTATAATTGTTTTGT 58.308 29.630 0.00 0.00 0.00 2.83
4474 5160 9.180678 CTCTGTTTGTGGTATAATTGTTTTGTC 57.819 33.333 0.00 0.00 0.00 3.18
4475 5161 8.908903 TCTGTTTGTGGTATAATTGTTTTGTCT 58.091 29.630 0.00 0.00 0.00 3.41
4476 5162 9.528018 CTGTTTGTGGTATAATTGTTTTGTCTT 57.472 29.630 0.00 0.00 0.00 3.01
4477 5163 9.877178 TGTTTGTGGTATAATTGTTTTGTCTTT 57.123 25.926 0.00 0.00 0.00 2.52
4524 5210 9.703892 ATATATTTGTGAGAGCTTAGATGTGAC 57.296 33.333 0.00 0.00 0.00 3.67
4525 5211 4.871933 TTGTGAGAGCTTAGATGTGACA 57.128 40.909 0.00 0.00 0.00 3.58
4526 5212 5.411831 TTGTGAGAGCTTAGATGTGACAT 57.588 39.130 0.00 0.00 0.00 3.06
4527 5213 5.003692 TGTGAGAGCTTAGATGTGACATC 57.996 43.478 17.46 17.46 0.00 3.06
4528 5214 4.142071 TGTGAGAGCTTAGATGTGACATCC 60.142 45.833 21.05 6.69 0.00 3.51
4529 5215 4.099266 GTGAGAGCTTAGATGTGACATCCT 59.901 45.833 21.05 11.37 0.00 3.24
4530 5216 4.713814 TGAGAGCTTAGATGTGACATCCTT 59.286 41.667 21.05 7.22 0.00 3.36
4531 5217 5.188555 TGAGAGCTTAGATGTGACATCCTTT 59.811 40.000 21.05 7.07 0.00 3.11
4532 5218 6.381133 TGAGAGCTTAGATGTGACATCCTTTA 59.619 38.462 21.05 5.51 0.00 1.85
4533 5219 7.093333 TGAGAGCTTAGATGTGACATCCTTTAA 60.093 37.037 21.05 12.48 0.00 1.52
4534 5220 7.624549 AGAGCTTAGATGTGACATCCTTTAAA 58.375 34.615 21.05 8.00 0.00 1.52
4535 5221 8.103305 AGAGCTTAGATGTGACATCCTTTAAAA 58.897 33.333 21.05 6.46 0.00 1.52
4536 5222 8.635765 AGCTTAGATGTGACATCCTTTAAAAA 57.364 30.769 21.05 4.95 0.00 1.94
4537 5223 8.515414 AGCTTAGATGTGACATCCTTTAAAAAC 58.485 33.333 21.05 6.99 0.00 2.43
4538 5224 8.296713 GCTTAGATGTGACATCCTTTAAAAACA 58.703 33.333 21.05 0.00 0.00 2.83
4541 5227 8.641498 AGATGTGACATCCTTTAAAAACATCT 57.359 30.769 21.05 8.71 44.92 2.90
4542 5228 9.739276 AGATGTGACATCCTTTAAAAACATCTA 57.261 29.630 21.05 0.00 46.74 1.98
4558 5244 8.731275 AAAACATCTATATGTGAATTGGACGA 57.269 30.769 0.00 0.00 45.79 4.20
4559 5245 8.731275 AAACATCTATATGTGAATTGGACGAA 57.269 30.769 0.00 0.00 45.79 3.85
4560 5246 7.715265 ACATCTATATGTGAATTGGACGAAC 57.285 36.000 0.00 0.00 44.79 3.95
4561 5247 7.500992 ACATCTATATGTGAATTGGACGAACT 58.499 34.615 0.00 0.00 44.79 3.01
4562 5248 7.439356 ACATCTATATGTGAATTGGACGAACTG 59.561 37.037 0.00 0.00 44.79 3.16
4563 5249 6.873997 TCTATATGTGAATTGGACGAACTGT 58.126 36.000 0.00 0.00 0.00 3.55
4564 5250 7.327975 TCTATATGTGAATTGGACGAACTGTT 58.672 34.615 0.00 0.00 0.00 3.16
4565 5251 6.817765 ATATGTGAATTGGACGAACTGTTT 57.182 33.333 0.00 0.00 0.00 2.83
4566 5252 4.974368 TGTGAATTGGACGAACTGTTTT 57.026 36.364 0.00 0.00 0.00 2.43
4567 5253 5.317733 TGTGAATTGGACGAACTGTTTTT 57.682 34.783 0.00 0.00 0.00 1.94
4568 5254 5.098893 TGTGAATTGGACGAACTGTTTTTG 58.901 37.500 0.00 0.00 0.00 2.44
4569 5255 5.099575 GTGAATTGGACGAACTGTTTTTGT 58.900 37.500 0.00 0.00 0.00 2.83
4570 5256 5.575218 GTGAATTGGACGAACTGTTTTTGTT 59.425 36.000 0.00 0.00 0.00 2.83
4571 5257 6.090223 GTGAATTGGACGAACTGTTTTTGTTT 59.910 34.615 0.00 0.00 0.00 2.83
4572 5258 6.647067 TGAATTGGACGAACTGTTTTTGTTTT 59.353 30.769 0.00 0.00 0.00 2.43
4573 5259 7.813148 TGAATTGGACGAACTGTTTTTGTTTTA 59.187 29.630 0.00 0.00 0.00 1.52
4574 5260 7.749539 ATTGGACGAACTGTTTTTGTTTTAG 57.250 32.000 0.00 0.00 0.00 1.85
4575 5261 5.642686 TGGACGAACTGTTTTTGTTTTAGG 58.357 37.500 0.00 0.00 0.00 2.69
4576 5262 5.415077 TGGACGAACTGTTTTTGTTTTAGGA 59.585 36.000 0.00 0.00 0.00 2.94
4577 5263 5.740569 GGACGAACTGTTTTTGTTTTAGGAC 59.259 40.000 0.00 0.00 0.00 3.85
4578 5264 6.256912 ACGAACTGTTTTTGTTTTAGGACA 57.743 33.333 0.00 0.00 0.00 4.02
4579 5265 6.859017 ACGAACTGTTTTTGTTTTAGGACAT 58.141 32.000 0.00 0.00 0.00 3.06
4580 5266 6.750039 ACGAACTGTTTTTGTTTTAGGACATG 59.250 34.615 0.00 0.00 0.00 3.21
4581 5267 6.750039 CGAACTGTTTTTGTTTTAGGACATGT 59.250 34.615 0.00 0.00 0.00 3.21
4582 5268 7.044314 CGAACTGTTTTTGTTTTAGGACATGTC 60.044 37.037 17.91 17.91 0.00 3.06
4583 5269 7.404671 ACTGTTTTTGTTTTAGGACATGTCT 57.595 32.000 24.50 13.31 0.00 3.41
4584 5270 7.257722 ACTGTTTTTGTTTTAGGACATGTCTG 58.742 34.615 24.50 1.82 0.00 3.51
4585 5271 7.122055 ACTGTTTTTGTTTTAGGACATGTCTGA 59.878 33.333 24.50 10.63 0.00 3.27
4586 5272 7.831753 TGTTTTTGTTTTAGGACATGTCTGAA 58.168 30.769 24.50 15.68 0.00 3.02
4587 5273 8.474025 TGTTTTTGTTTTAGGACATGTCTGAAT 58.526 29.630 24.50 11.32 0.00 2.57
4588 5274 8.968242 GTTTTTGTTTTAGGACATGTCTGAATC 58.032 33.333 24.50 14.94 0.00 2.52
4589 5275 8.463930 TTTTGTTTTAGGACATGTCTGAATCT 57.536 30.769 24.50 14.97 0.00 2.40
4590 5276 7.439157 TTGTTTTAGGACATGTCTGAATCTG 57.561 36.000 24.50 0.00 0.00 2.90
4591 5277 6.533730 TGTTTTAGGACATGTCTGAATCTGT 58.466 36.000 24.50 3.43 0.00 3.41
4592 5278 6.427853 TGTTTTAGGACATGTCTGAATCTGTG 59.572 38.462 24.50 0.00 0.00 3.66
4593 5279 5.745312 TTAGGACATGTCTGAATCTGTGT 57.255 39.130 24.50 1.11 0.00 3.72
4594 5280 4.630644 AGGACATGTCTGAATCTGTGTT 57.369 40.909 24.50 0.00 0.00 3.32
4595 5281 4.321718 AGGACATGTCTGAATCTGTGTTG 58.678 43.478 24.50 0.00 0.00 3.33
4596 5282 3.120060 GGACATGTCTGAATCTGTGTTGC 60.120 47.826 24.50 0.00 0.00 4.17
4597 5283 3.748083 ACATGTCTGAATCTGTGTTGCT 58.252 40.909 0.00 0.00 0.00 3.91
4598 5284 3.501062 ACATGTCTGAATCTGTGTTGCTG 59.499 43.478 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.751643 AAGTGGTTTTCGCTGCTGGT 60.752 50.000 0.00 0.00 36.17 4.00
1 2 0.318107 CAAGTGGTTTTCGCTGCTGG 60.318 55.000 0.00 0.00 36.17 4.85
2 3 0.936297 GCAAGTGGTTTTCGCTGCTG 60.936 55.000 0.00 0.00 36.17 4.41
3 4 1.360192 GCAAGTGGTTTTCGCTGCT 59.640 52.632 0.00 0.00 36.17 4.24
4 5 1.661509 GGCAAGTGGTTTTCGCTGC 60.662 57.895 0.00 0.00 36.17 5.25
5 6 0.385390 AAGGCAAGTGGTTTTCGCTG 59.615 50.000 0.00 0.00 36.17 5.18
6 7 0.668535 GAAGGCAAGTGGTTTTCGCT 59.331 50.000 0.00 0.00 37.93 4.93
7 8 0.383949 TGAAGGCAAGTGGTTTTCGC 59.616 50.000 0.00 0.00 0.00 4.70
8 9 2.293122 TGATGAAGGCAAGTGGTTTTCG 59.707 45.455 0.00 0.00 0.00 3.46
9 10 4.525912 ATGATGAAGGCAAGTGGTTTTC 57.474 40.909 0.00 0.00 0.00 2.29
10 11 4.262592 GGAATGATGAAGGCAAGTGGTTTT 60.263 41.667 0.00 0.00 0.00 2.43
11 12 3.259123 GGAATGATGAAGGCAAGTGGTTT 59.741 43.478 0.00 0.00 0.00 3.27
12 13 2.827921 GGAATGATGAAGGCAAGTGGTT 59.172 45.455 0.00 0.00 0.00 3.67
13 14 2.450476 GGAATGATGAAGGCAAGTGGT 58.550 47.619 0.00 0.00 0.00 4.16
14 15 1.753073 GGGAATGATGAAGGCAAGTGG 59.247 52.381 0.00 0.00 0.00 4.00
15 16 2.449464 TGGGAATGATGAAGGCAAGTG 58.551 47.619 0.00 0.00 0.00 3.16
16 17 2.905415 TGGGAATGATGAAGGCAAGT 57.095 45.000 0.00 0.00 0.00 3.16
17 18 4.442472 GGAAATGGGAATGATGAAGGCAAG 60.442 45.833 0.00 0.00 0.00 4.01
18 19 3.451902 GGAAATGGGAATGATGAAGGCAA 59.548 43.478 0.00 0.00 0.00 4.52
19 20 3.033184 GGAAATGGGAATGATGAAGGCA 58.967 45.455 0.00 0.00 0.00 4.75
20 21 2.366590 GGGAAATGGGAATGATGAAGGC 59.633 50.000 0.00 0.00 0.00 4.35
21 22 2.624838 CGGGAAATGGGAATGATGAAGG 59.375 50.000 0.00 0.00 0.00 3.46
22 23 3.290710 ACGGGAAATGGGAATGATGAAG 58.709 45.455 0.00 0.00 0.00 3.02
23 24 3.380471 ACGGGAAATGGGAATGATGAA 57.620 42.857 0.00 0.00 0.00 2.57
24 25 3.201045 TGTACGGGAAATGGGAATGATGA 59.799 43.478 0.00 0.00 0.00 2.92
25 26 3.550820 TGTACGGGAAATGGGAATGATG 58.449 45.455 0.00 0.00 0.00 3.07
26 27 3.943671 TGTACGGGAAATGGGAATGAT 57.056 42.857 0.00 0.00 0.00 2.45
27 28 3.244946 TGTTGTACGGGAAATGGGAATGA 60.245 43.478 0.00 0.00 0.00 2.57
28 29 3.085533 TGTTGTACGGGAAATGGGAATG 58.914 45.455 0.00 0.00 0.00 2.67
29 30 3.443145 TGTTGTACGGGAAATGGGAAT 57.557 42.857 0.00 0.00 0.00 3.01
30 31 2.953284 TGTTGTACGGGAAATGGGAA 57.047 45.000 0.00 0.00 0.00 3.97
31 32 2.306219 TGATGTTGTACGGGAAATGGGA 59.694 45.455 0.00 0.00 0.00 4.37
32 33 2.717390 TGATGTTGTACGGGAAATGGG 58.283 47.619 0.00 0.00 0.00 4.00
36 37 2.004017 GCGATGATGTTGTACGGGAAA 58.996 47.619 0.00 0.00 0.00 3.13
39 40 0.930310 CAGCGATGATGTTGTACGGG 59.070 55.000 0.00 0.00 0.00 5.28
57 58 1.816224 GGGATTTTCTTAGGCGCAACA 59.184 47.619 10.83 0.00 0.00 3.33
59 60 2.091541 CTGGGATTTTCTTAGGCGCAA 58.908 47.619 10.83 0.00 0.00 4.85
63 64 2.159379 CGCAACTGGGATTTTCTTAGGC 60.159 50.000 0.00 0.00 0.00 3.93
90 91 0.036765 ATTTCCGTCCAGCTTACGCA 60.037 50.000 11.94 0.00 39.00 5.24
99 100 1.294138 GTCACCCGATTTCCGTCCA 59.706 57.895 0.00 0.00 36.31 4.02
103 104 0.739813 GTCCTGTCACCCGATTTCCG 60.740 60.000 0.00 0.00 38.18 4.30
105 106 2.009774 CATGTCCTGTCACCCGATTTC 58.990 52.381 0.00 0.00 0.00 2.17
136 137 3.041940 CGGTTGCCACAGGACGAC 61.042 66.667 0.00 0.00 0.00 4.34
137 138 3.228017 TCGGTTGCCACAGGACGA 61.228 61.111 0.00 0.00 0.00 4.20
138 139 3.041940 GTCGGTTGCCACAGGACG 61.042 66.667 0.00 0.00 0.00 4.79
139 140 1.098712 TTTGTCGGTTGCCACAGGAC 61.099 55.000 4.90 4.90 0.00 3.85
148 149 6.175087 CGAAAAAGTTCAATTTTGTCGGTTG 58.825 36.000 9.54 0.00 33.75 3.77
171 172 2.417516 CGCAGTATCAGGGTCCCG 59.582 66.667 0.99 0.00 0.00 5.14
175 176 2.687200 TGGGCGCAGTATCAGGGT 60.687 61.111 10.83 0.00 0.00 4.34
176 177 2.109799 CTGGGCGCAGTATCAGGG 59.890 66.667 21.92 0.00 0.00 4.45
179 180 2.434843 CCCTCTGGGCGCAGTATCA 61.435 63.158 27.76 9.93 35.35 2.15
180 181 2.423446 CCCTCTGGGCGCAGTATC 59.577 66.667 27.76 0.00 35.35 2.24
188 189 9.831253 TACTCGTTTAGTTAAAACCCTCTGGGC 62.831 44.444 1.99 0.00 43.90 5.36
189 190 5.744007 ACTCGTTTAGTTAAAACCCTCTGGG 60.744 44.000 0.32 0.32 43.90 4.45
193 194 5.349817 GGCTACTCGTTTAGTTAAAACCCTC 59.650 44.000 0.00 0.00 43.90 4.30
202 203 1.553704 CCTGGGGCTACTCGTTTAGTT 59.446 52.381 0.00 0.00 39.80 2.24
203 204 1.192428 CCTGGGGCTACTCGTTTAGT 58.808 55.000 0.00 0.00 42.62 2.24
204 205 0.179081 GCCTGGGGCTACTCGTTTAG 60.179 60.000 0.80 0.00 46.69 1.85
205 206 1.902556 GCCTGGGGCTACTCGTTTA 59.097 57.895 0.80 0.00 46.69 2.01
206 207 2.669240 GCCTGGGGCTACTCGTTT 59.331 61.111 0.80 0.00 46.69 3.60
244 245 3.328637 TCATATCCAGTGGGTGATCATGG 59.671 47.826 9.92 1.79 34.93 3.66
317 318 6.741992 TGTTTAGGAGACACAGCAATAATG 57.258 37.500 0.00 0.00 0.00 1.90
377 382 3.382227 TCTTATTCCTACGTTCCATGCGA 59.618 43.478 0.00 0.00 0.00 5.10
378 383 3.713288 TCTTATTCCTACGTTCCATGCG 58.287 45.455 0.00 0.00 0.00 4.73
394 399 8.109634 AGTGTCAACAAATTGGGAGTATCTTAT 58.890 33.333 0.00 0.00 36.39 1.73
413 418 0.253044 GGCTATCCCTGCAGTGTCAA 59.747 55.000 13.81 0.00 0.00 3.18
521 531 7.724305 TTAGGACGCAATTATGAAGTTATCC 57.276 36.000 0.00 0.00 0.00 2.59
558 568 1.207329 ACTTCTTCGTCCTGGTATGCC 59.793 52.381 0.00 0.00 0.00 4.40
587 599 9.383519 GACACAATTATGAAGTTATCTCTTGGA 57.616 33.333 0.00 0.00 0.00 3.53
737 749 7.450074 AGCCCGACAATATGTGAATATTCTTA 58.550 34.615 16.24 5.93 0.00 2.10
739 751 5.869579 AGCCCGACAATATGTGAATATTCT 58.130 37.500 16.24 0.00 0.00 2.40
752 764 0.693049 AACAGGAAGAGCCCGACAAT 59.307 50.000 0.00 0.00 37.37 2.71
786 798 2.038975 AGGGGAAGCTCCTACGCA 59.961 61.111 0.00 0.00 36.57 5.24
1027 1044 6.978659 TCAGTATCTTTACGCAGAATCGAAAT 59.021 34.615 0.00 0.00 33.32 2.17
1130 1154 2.273179 CGGGTGGAGGTCGTCAGAA 61.273 63.158 0.00 0.00 0.00 3.02
1170 1200 1.073923 GTCAAGGTTGAGGTGACCCAT 59.926 52.381 0.00 0.00 37.98 4.00
1341 1371 1.401552 CACAGGTGGCAATGTTATCCG 59.598 52.381 3.99 0.00 0.00 4.18
1504 1536 1.739466 CTAACAATGCGGTGCTGTCAT 59.261 47.619 0.00 0.00 0.00 3.06
1535 1567 4.142403 GCAGTTTGCTCCTAATATTGTGCA 60.142 41.667 0.00 0.00 40.96 4.57
1540 1572 3.633986 GCAGGCAGTTTGCTCCTAATATT 59.366 43.478 0.67 0.00 44.28 1.28
1543 1577 1.272092 TGCAGGCAGTTTGCTCCTAAT 60.272 47.619 0.67 0.00 44.28 1.73
1582 1616 1.065854 ACAAAAGGAGGATGGAGCTCG 60.066 52.381 7.83 0.00 0.00 5.03
1619 1653 9.676195 TTTGTATCAATGTTTACACAGTTCATG 57.324 29.630 0.00 0.00 35.94 3.07
1642 1677 7.435192 TCGCATGATGTGTTCTAGTATACTTTG 59.565 37.037 11.40 5.05 0.00 2.77
1664 1699 1.153568 GCTGCCTCATACAGTCGCA 60.154 57.895 0.00 0.00 37.47 5.10
1681 1716 1.017387 CAGTTTTCGCCTATCCCTGC 58.983 55.000 0.00 0.00 0.00 4.85
1689 1724 2.095059 ACGTATCGTACAGTTTTCGCCT 60.095 45.455 0.00 0.00 38.73 5.52
1711 1746 3.674997 GACAAAATGTAGCTGGTCCTCA 58.325 45.455 0.00 0.00 0.00 3.86
1735 1770 9.191995 GTTATTTGTCAGTTTCCATTTAACCAG 57.808 33.333 0.00 0.00 0.00 4.00
1772 1807 3.696548 GGATGAAATGGGGACTGAACTTC 59.303 47.826 0.00 0.00 0.00 3.01
1801 1845 2.507484 ACTGGTGTCATTGTGGTGATG 58.493 47.619 0.00 0.00 0.00 3.07
1808 1852 6.109156 TCATTGTAGTACTGGTGTCATTGT 57.891 37.500 5.39 0.00 0.00 2.71
1828 1872 6.373779 CGACAAGTGCTAAAATGACTTTCAT 58.626 36.000 0.00 0.00 39.09 2.57
1833 1877 3.740115 ACCGACAAGTGCTAAAATGACT 58.260 40.909 0.00 0.00 0.00 3.41
1868 1914 7.624360 ATGATTACGAATGTAGCAGGAAAAA 57.376 32.000 0.00 0.00 0.00 1.94
1971 2020 9.175060 CGTTGTGTAGATACTTCAGAATATCTG 57.825 37.037 17.18 0.88 45.59 2.90
2122 2171 4.981674 ACAATGATGCAGTTGTTAAAACCG 59.018 37.500 8.57 0.00 35.13 4.44
2148 2199 3.181455 TGCTATGTCCACATGTACCCATC 60.181 47.826 0.00 0.00 37.15 3.51
2182 2233 7.083230 GTCAGAGAATACGCCTTAGTAATACC 58.917 42.308 0.00 0.00 0.00 2.73
2198 2701 2.183679 GAGGTCACCCTGTCAGAGAAT 58.816 52.381 0.00 0.00 42.86 2.40
2254 2762 6.720112 ACATTTTATATGCACAGAAGCCAT 57.280 33.333 0.00 0.00 0.00 4.40
2257 2765 7.035004 TGGAAACATTTTATATGCACAGAAGC 58.965 34.615 0.00 0.00 33.40 3.86
2673 3284 3.555586 GGCCAATATTGCATCCATTCACC 60.556 47.826 10.11 0.00 0.00 4.02
2756 3371 7.330946 TGTCAGACATTACACAATTAGTACTGC 59.669 37.037 5.39 0.00 0.00 4.40
2835 3452 0.696501 GGCCACCCTCCTTACTTCAA 59.303 55.000 0.00 0.00 0.00 2.69
3148 3765 3.044986 CACAACAGTCTTGATTTTGCCG 58.955 45.455 0.00 0.00 0.00 5.69
3232 3849 2.562635 CAGGAGACCTTCTCATGCATG 58.437 52.381 21.07 21.07 46.23 4.06
3251 3868 1.463553 TTCACGAGCTCTCTGGCACA 61.464 55.000 12.85 0.00 34.17 4.57
3343 3960 1.947456 AGAAAGTTCCGGTGCTTGTTC 59.053 47.619 12.51 8.47 0.00 3.18
3397 4014 4.933330 TGTGCTTCGAGTGGAGATTATAC 58.067 43.478 0.00 0.00 0.00 1.47
3437 4054 4.081087 ACGGTTGTAGGCATAGAGACAAAT 60.081 41.667 0.00 0.00 33.82 2.32
3563 4180 3.749088 TGACAACACAAAACGACTTCAGT 59.251 39.130 0.00 0.00 0.00 3.41
3571 4188 3.063670 TCAGCATGACAACACAAAACG 57.936 42.857 0.00 0.00 42.56 3.60
3617 4234 7.665559 ACTTCAGTGCCTTCATATCAAAAGTAA 59.334 33.333 0.00 0.00 0.00 2.24
3618 4235 7.168219 ACTTCAGTGCCTTCATATCAAAAGTA 58.832 34.615 0.00 0.00 0.00 2.24
3619 4236 6.006449 ACTTCAGTGCCTTCATATCAAAAGT 58.994 36.000 0.00 0.00 0.00 2.66
3654 4272 2.380064 AAGGGGAAAACAGCATGACA 57.620 45.000 0.00 0.00 39.69 3.58
3655 4273 2.627699 TGAAAGGGGAAAACAGCATGAC 59.372 45.455 0.00 0.00 39.69 3.06
3656 4274 2.627699 GTGAAAGGGGAAAACAGCATGA 59.372 45.455 0.00 0.00 39.69 3.07
3706 4328 8.552296 AGTTTACATCATGGATTTCTCCTTACT 58.448 33.333 0.00 0.00 42.59 2.24
3740 4362 7.041235 GCATACAGTACCTTACTACTACTCAGG 60.041 44.444 0.00 0.00 37.23 3.86
3741 4363 7.716123 AGCATACAGTACCTTACTACTACTCAG 59.284 40.741 0.00 0.00 37.23 3.35
3742 4364 7.498239 CAGCATACAGTACCTTACTACTACTCA 59.502 40.741 0.00 0.00 37.23 3.41
3743 4365 7.498570 ACAGCATACAGTACCTTACTACTACTC 59.501 40.741 0.00 0.00 37.23 2.59
3744 4366 7.282675 CACAGCATACAGTACCTTACTACTACT 59.717 40.741 0.00 0.00 37.23 2.57
3745 4367 7.281774 TCACAGCATACAGTACCTTACTACTAC 59.718 40.741 0.00 0.00 37.23 2.73
3746 4368 7.341030 TCACAGCATACAGTACCTTACTACTA 58.659 38.462 0.00 0.00 37.23 1.82
3747 4369 6.185511 TCACAGCATACAGTACCTTACTACT 58.814 40.000 0.00 0.00 37.23 2.57
3748 4370 6.095160 ACTCACAGCATACAGTACCTTACTAC 59.905 42.308 0.00 0.00 37.23 2.73
3749 4371 6.185511 ACTCACAGCATACAGTACCTTACTA 58.814 40.000 0.00 0.00 37.23 1.82
3750 4372 5.017490 ACTCACAGCATACAGTACCTTACT 58.983 41.667 0.00 0.00 40.28 2.24
3791 4418 3.081061 TCGCAGCATTACAAGTGGAAAT 58.919 40.909 0.00 0.00 0.00 2.17
3801 4460 4.826500 CTGATTAAGTGTCGCAGCATTAC 58.173 43.478 0.00 0.00 0.00 1.89
3818 4477 0.546122 TATGCCCGACCTTGCTGATT 59.454 50.000 0.00 0.00 0.00 2.57
3899 4558 2.882137 TCGATTTTGTTTCCAGACCCAC 59.118 45.455 0.00 0.00 0.00 4.61
3935 4594 4.628963 TTGGTACTAGTTTCTTCCCCAC 57.371 45.455 0.00 0.00 0.00 4.61
3942 4601 6.060136 GGGTTTCTGTTTGGTACTAGTTTCT 58.940 40.000 0.00 0.00 0.00 2.52
3950 4609 1.241165 CCGGGGTTTCTGTTTGGTAC 58.759 55.000 0.00 0.00 0.00 3.34
3971 4630 4.860881 CTCTCCGCCCAGCCCCTA 62.861 72.222 0.00 0.00 0.00 3.53
4260 4944 0.376852 GCGTGCACAAAGTTGACTGA 59.623 50.000 18.64 0.00 0.00 3.41
4315 4999 4.003648 CCACTTTCTTTGATCCGCTACTT 58.996 43.478 0.00 0.00 0.00 2.24
4316 5000 3.260884 TCCACTTTCTTTGATCCGCTACT 59.739 43.478 0.00 0.00 0.00 2.57
4322 5006 5.787380 AGCATTTTCCACTTTCTTTGATCC 58.213 37.500 0.00 0.00 0.00 3.36
4324 5008 5.993441 CCAAGCATTTTCCACTTTCTTTGAT 59.007 36.000 0.00 0.00 0.00 2.57
4333 5019 5.813513 ATTTTCTCCAAGCATTTTCCACT 57.186 34.783 0.00 0.00 0.00 4.00
4360 5046 6.374417 TCAAAGGAAGGAGTATTTGTAGCT 57.626 37.500 0.00 0.00 34.88 3.32
4387 5073 3.985279 CACGTCTAGATGTGTCCGAAAAA 59.015 43.478 29.45 0.00 41.97 1.94
4388 5074 3.253921 TCACGTCTAGATGTGTCCGAAAA 59.746 43.478 33.64 17.29 45.84 2.29
4389 5075 2.815503 TCACGTCTAGATGTGTCCGAAA 59.184 45.455 33.64 17.90 45.84 3.46
4390 5076 2.161012 GTCACGTCTAGATGTGTCCGAA 59.839 50.000 33.64 18.50 45.84 4.30
4391 5077 1.736126 GTCACGTCTAGATGTGTCCGA 59.264 52.381 33.64 18.81 45.84 4.55
4392 5078 1.467342 TGTCACGTCTAGATGTGTCCG 59.533 52.381 33.64 18.01 45.84 4.79
4393 5079 3.784701 ATGTCACGTCTAGATGTGTCC 57.215 47.619 33.64 26.72 45.84 4.02
4394 5080 5.487153 ACTATGTCACGTCTAGATGTGTC 57.513 43.478 33.64 29.76 45.84 3.67
4395 5081 5.899120 AACTATGTCACGTCTAGATGTGT 57.101 39.130 33.64 22.33 45.84 3.72
4396 5082 7.418408 ACATAACTATGTCACGTCTAGATGTG 58.582 38.462 31.17 31.17 42.96 3.21
4397 5083 7.569639 ACATAACTATGTCACGTCTAGATGT 57.430 36.000 11.99 11.99 42.96 3.06
4431 5117 4.357325 ACAGAGTGGACATCAGGTTAGAT 58.643 43.478 0.00 0.00 0.00 1.98
4432 5118 3.779444 ACAGAGTGGACATCAGGTTAGA 58.221 45.455 0.00 0.00 0.00 2.10
4433 5119 4.543590 AACAGAGTGGACATCAGGTTAG 57.456 45.455 0.00 0.00 0.00 2.34
4434 5120 4.102524 ACAAACAGAGTGGACATCAGGTTA 59.897 41.667 0.00 0.00 0.00 2.85
4435 5121 3.117888 ACAAACAGAGTGGACATCAGGTT 60.118 43.478 0.00 0.00 0.00 3.50
4436 5122 2.439507 ACAAACAGAGTGGACATCAGGT 59.560 45.455 0.00 0.00 0.00 4.00
4437 5123 2.810274 CACAAACAGAGTGGACATCAGG 59.190 50.000 0.00 0.00 33.43 3.86
4446 5132 8.967218 CAAAACAATTATACCACAAACAGAGTG 58.033 33.333 0.00 0.00 36.76 3.51
4447 5133 8.691797 ACAAAACAATTATACCACAAACAGAGT 58.308 29.630 0.00 0.00 0.00 3.24
4448 5134 9.180678 GACAAAACAATTATACCACAAACAGAG 57.819 33.333 0.00 0.00 0.00 3.35
4449 5135 8.908903 AGACAAAACAATTATACCACAAACAGA 58.091 29.630 0.00 0.00 0.00 3.41
4450 5136 9.528018 AAGACAAAACAATTATACCACAAACAG 57.472 29.630 0.00 0.00 0.00 3.16
4451 5137 9.877178 AAAGACAAAACAATTATACCACAAACA 57.123 25.926 0.00 0.00 0.00 2.83
4498 5184 9.703892 GTCACATCTAAGCTCTCACAAATATAT 57.296 33.333 0.00 0.00 0.00 0.86
4499 5185 8.695456 TGTCACATCTAAGCTCTCACAAATATA 58.305 33.333 0.00 0.00 0.00 0.86
4500 5186 7.559486 TGTCACATCTAAGCTCTCACAAATAT 58.441 34.615 0.00 0.00 0.00 1.28
4501 5187 6.935167 TGTCACATCTAAGCTCTCACAAATA 58.065 36.000 0.00 0.00 0.00 1.40
4502 5188 5.798132 TGTCACATCTAAGCTCTCACAAAT 58.202 37.500 0.00 0.00 0.00 2.32
4503 5189 5.213891 TGTCACATCTAAGCTCTCACAAA 57.786 39.130 0.00 0.00 0.00 2.83
4504 5190 4.871933 TGTCACATCTAAGCTCTCACAA 57.128 40.909 0.00 0.00 0.00 3.33
4505 5191 4.142071 GGATGTCACATCTAAGCTCTCACA 60.142 45.833 17.46 0.00 0.00 3.58
4506 5192 4.099266 AGGATGTCACATCTAAGCTCTCAC 59.901 45.833 17.46 0.00 0.00 3.51
4507 5193 4.285020 AGGATGTCACATCTAAGCTCTCA 58.715 43.478 17.46 0.00 0.00 3.27
4508 5194 4.935352 AGGATGTCACATCTAAGCTCTC 57.065 45.455 17.46 0.00 0.00 3.20
4509 5195 5.690464 AAAGGATGTCACATCTAAGCTCT 57.310 39.130 17.46 2.09 0.00 4.09
4510 5196 7.849804 TTTAAAGGATGTCACATCTAAGCTC 57.150 36.000 17.46 0.00 0.00 4.09
4511 5197 8.515414 GTTTTTAAAGGATGTCACATCTAAGCT 58.485 33.333 17.46 3.19 0.00 3.74
4512 5198 8.296713 TGTTTTTAAAGGATGTCACATCTAAGC 58.703 33.333 17.46 0.73 0.00 3.09
4515 5201 9.739276 AGATGTTTTTAAAGGATGTCACATCTA 57.261 29.630 17.46 0.00 44.89 1.98
4516 5202 8.641498 AGATGTTTTTAAAGGATGTCACATCT 57.359 30.769 17.46 11.06 42.98 2.90
4532 5218 9.173021 TCGTCCAATTCACATATAGATGTTTTT 57.827 29.630 0.00 0.00 44.18 1.94
4533 5219 8.731275 TCGTCCAATTCACATATAGATGTTTT 57.269 30.769 0.00 0.00 44.18 2.43
4534 5220 8.612619 GTTCGTCCAATTCACATATAGATGTTT 58.387 33.333 0.00 0.00 44.18 2.83
4535 5221 7.987458 AGTTCGTCCAATTCACATATAGATGTT 59.013 33.333 0.00 0.00 44.18 2.71
4537 5223 7.439356 ACAGTTCGTCCAATTCACATATAGATG 59.561 37.037 0.00 0.00 39.16 2.90
4538 5224 7.500992 ACAGTTCGTCCAATTCACATATAGAT 58.499 34.615 0.00 0.00 0.00 1.98
4539 5225 6.873997 ACAGTTCGTCCAATTCACATATAGA 58.126 36.000 0.00 0.00 0.00 1.98
4540 5226 7.539712 AACAGTTCGTCCAATTCACATATAG 57.460 36.000 0.00 0.00 0.00 1.31
4541 5227 7.915293 AAACAGTTCGTCCAATTCACATATA 57.085 32.000 0.00 0.00 0.00 0.86
4542 5228 6.817765 AAACAGTTCGTCCAATTCACATAT 57.182 33.333 0.00 0.00 0.00 1.78
4543 5229 6.627395 AAAACAGTTCGTCCAATTCACATA 57.373 33.333 0.00 0.00 0.00 2.29
4544 5230 5.514274 AAAACAGTTCGTCCAATTCACAT 57.486 34.783 0.00 0.00 0.00 3.21
4545 5231 4.974368 AAAACAGTTCGTCCAATTCACA 57.026 36.364 0.00 0.00 0.00 3.58
4546 5232 5.099575 ACAAAAACAGTTCGTCCAATTCAC 58.900 37.500 0.00 0.00 0.00 3.18
4547 5233 5.317733 ACAAAAACAGTTCGTCCAATTCA 57.682 34.783 0.00 0.00 0.00 2.57
4548 5234 6.641176 AAACAAAAACAGTTCGTCCAATTC 57.359 33.333 0.00 0.00 0.00 2.17
4549 5235 7.276878 CCTAAAACAAAAACAGTTCGTCCAATT 59.723 33.333 0.00 0.00 0.00 2.32
4550 5236 6.754675 CCTAAAACAAAAACAGTTCGTCCAAT 59.245 34.615 0.00 0.00 0.00 3.16
4551 5237 6.072064 TCCTAAAACAAAAACAGTTCGTCCAA 60.072 34.615 0.00 0.00 0.00 3.53
4552 5238 5.415077 TCCTAAAACAAAAACAGTTCGTCCA 59.585 36.000 0.00 0.00 0.00 4.02
4553 5239 5.740569 GTCCTAAAACAAAAACAGTTCGTCC 59.259 40.000 0.00 0.00 0.00 4.79
4554 5240 6.316319 TGTCCTAAAACAAAAACAGTTCGTC 58.684 36.000 0.00 0.00 0.00 4.20
4555 5241 6.256912 TGTCCTAAAACAAAAACAGTTCGT 57.743 33.333 0.00 0.00 0.00 3.85
4556 5242 6.750039 ACATGTCCTAAAACAAAAACAGTTCG 59.250 34.615 0.00 0.00 31.81 3.95
4557 5243 7.973944 AGACATGTCCTAAAACAAAAACAGTTC 59.026 33.333 22.21 0.00 31.81 3.01
4558 5244 7.759433 CAGACATGTCCTAAAACAAAAACAGTT 59.241 33.333 22.21 0.00 31.81 3.16
4559 5245 7.122055 TCAGACATGTCCTAAAACAAAAACAGT 59.878 33.333 22.21 0.00 31.81 3.55
4560 5246 7.479980 TCAGACATGTCCTAAAACAAAAACAG 58.520 34.615 22.21 0.00 31.81 3.16
4561 5247 7.397892 TCAGACATGTCCTAAAACAAAAACA 57.602 32.000 22.21 0.00 31.81 2.83
4562 5248 8.871686 ATTCAGACATGTCCTAAAACAAAAAC 57.128 30.769 22.21 0.00 31.81 2.43
4563 5249 8.912988 AGATTCAGACATGTCCTAAAACAAAAA 58.087 29.630 22.21 2.99 31.81 1.94
4564 5250 8.352201 CAGATTCAGACATGTCCTAAAACAAAA 58.648 33.333 22.21 4.44 31.81 2.44
4565 5251 7.502226 ACAGATTCAGACATGTCCTAAAACAAA 59.498 33.333 22.21 5.88 31.81 2.83
4566 5252 6.998074 ACAGATTCAGACATGTCCTAAAACAA 59.002 34.615 22.21 5.37 31.81 2.83
4567 5253 6.427853 CACAGATTCAGACATGTCCTAAAACA 59.572 38.462 22.21 0.37 0.00 2.83
4568 5254 6.428159 ACACAGATTCAGACATGTCCTAAAAC 59.572 38.462 22.21 12.19 0.00 2.43
4569 5255 6.533730 ACACAGATTCAGACATGTCCTAAAA 58.466 36.000 22.21 11.50 0.00 1.52
4570 5256 6.114187 ACACAGATTCAGACATGTCCTAAA 57.886 37.500 22.21 13.88 0.00 1.85
4571 5257 5.745312 ACACAGATTCAGACATGTCCTAA 57.255 39.130 22.21 16.31 0.00 2.69
4572 5258 5.482006 CAACACAGATTCAGACATGTCCTA 58.518 41.667 22.21 7.93 0.00 2.94
4573 5259 4.321718 CAACACAGATTCAGACATGTCCT 58.678 43.478 22.21 8.90 0.00 3.85
4574 5260 3.120060 GCAACACAGATTCAGACATGTCC 60.120 47.826 22.21 6.58 0.00 4.02
4575 5261 3.750130 AGCAACACAGATTCAGACATGTC 59.250 43.478 18.47 18.47 0.00 3.06
4576 5262 3.501062 CAGCAACACAGATTCAGACATGT 59.499 43.478 0.00 0.00 0.00 3.21
4577 5263 4.079665 CAGCAACACAGATTCAGACATG 57.920 45.455 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.