Multiple sequence alignment - TraesCS3D01G437400

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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 TraesCS3D01G437400 chr3D 100.000 3326 0 0 1 3326 548675874 548672549 0.000000e+00 6143.0
1 TraesCS3D01G437400 chr3D 84.463 1062 98 30 1032 2040 548635668 548634621 0.000000e+00 985.0
2 TraesCS3D01G437400 chr3D 83.459 133 20 2 1064 1195 548965190 548965321 4.510000e-24 122.0
3 TraesCS3D01G437400 chr3D 79.439 107 13 7 137 241 527693813 527693912 2.140000e-07 67.6
4 TraesCS3D01G437400 chr3A 88.695 2123 151 34 1 2077 686163927 686161848 0.000000e+00 2508.0
5 TraesCS3D01G437400 chr3A 87.146 1058 97 20 2290 3326 686161373 686160334 0.000000e+00 1164.0
6 TraesCS3D01G437400 chr3A 84.652 1062 101 33 1032 2046 686158220 686157174 0.000000e+00 1002.0
7 TraesCS3D01G437400 chr3A 83.333 132 22 0 1064 1195 686254110 686254241 4.510000e-24 122.0
8 TraesCS3D01G437400 chr3A 73.653 167 34 7 96 255 732636968 732637131 4.640000e-04 56.5
9 TraesCS3D01G437400 chr3B 87.070 2065 196 34 11 2039 727465307 727463278 0.000000e+00 2268.0
10 TraesCS3D01G437400 chr3B 93.007 715 43 4 2606 3318 727425125 727424416 0.000000e+00 1037.0
11 TraesCS3D01G437400 chr3B 93.558 326 12 4 2287 2610 727452884 727452566 8.350000e-131 477.0
12 TraesCS3D01G437400 chr3B 82.340 470 62 16 1583 2046 727422386 727421932 4.020000e-104 388.0
13 TraesCS3D01G437400 chr3B 93.284 134 9 0 2039 2172 727453031 727452898 7.280000e-47 198.0
14 TraesCS3D01G437400 chr3B 72.790 724 132 41 1306 1989 728199408 728200106 5.670000e-43 185.0
15 TraesCS3D01G437400 chr5D 97.196 107 3 0 2182 2288 58137570 58137676 7.330000e-42 182.0
16 TraesCS3D01G437400 chr6D 96.330 109 4 0 2182 2290 278641623 278641731 2.640000e-41 180.0
17 TraesCS3D01G437400 chr7A 93.860 114 7 0 2182 2295 19217293 19217406 4.410000e-39 172.0
18 TraesCS3D01G437400 chr7A 95.327 107 5 0 2182 2288 572868075 572867969 1.590000e-38 171.0
19 TraesCS3D01G437400 chr7A 94.444 108 6 0 2182 2289 184652397 184652504 2.050000e-37 167.0
20 TraesCS3D01G437400 chr5A 93.860 114 7 0 2181 2294 656658900 656658787 4.410000e-39 172.0
21 TraesCS3D01G437400 chr5A 92.174 115 9 0 2180 2294 577925314 577925428 2.660000e-36 163.0
22 TraesCS3D01G437400 chr1A 91.129 124 10 1 2182 2305 466906450 466906328 2.050000e-37 167.0
23 TraesCS3D01G437400 chr7D 90.833 120 11 0 2172 2291 598012941 598013060 9.550000e-36 161.0
24 TraesCS3D01G437400 chr7D 77.931 145 21 10 197 332 162676637 162676779 2.750000e-11 80.5
25 TraesCS3D01G437400 chr5B 84.127 126 15 3 167 290 112535021 112535143 2.100000e-22 117.0
26 TraesCS3D01G437400 chr2B 78.022 182 30 10 195 371 29863793 29863617 4.540000e-19 106.0
27 TraesCS3D01G437400 chr1D 74.170 271 58 11 127 392 420910357 420910094 5.870000e-18 102.0
28 TraesCS3D01G437400 chr2D 75.000 204 33 16 197 390 423511336 423511531 9.890000e-11 78.7
29 TraesCS3D01G437400 chr2D 74.874 199 33 15 214 400 304259487 304259680 1.280000e-09 75.0


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 TraesCS3D01G437400 chr3D 548672549 548675874 3325 True 6143.0 6143 100.0000 1 3326 1 chr3D.!!$R2 3325
1 TraesCS3D01G437400 chr3D 548634621 548635668 1047 True 985.0 985 84.4630 1032 2040 1 chr3D.!!$R1 1008
2 TraesCS3D01G437400 chr3A 686157174 686163927 6753 True 1558.0 2508 86.8310 1 3326 3 chr3A.!!$R1 3325
3 TraesCS3D01G437400 chr3B 727463278 727465307 2029 True 2268.0 2268 87.0700 11 2039 1 chr3B.!!$R1 2028
4 TraesCS3D01G437400 chr3B 727421932 727425125 3193 True 712.5 1037 87.6735 1583 3318 2 chr3B.!!$R2 1735

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
928 972 0.816825 ATGCAAATCCGCTCATCGCT 60.817 50.0 0.0 0.0 36.73 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2854 4502 0.036732 TAGCTTGGGTCAGTGCTTGG 59.963 55.0 0.0 0.0 37.02 3.61 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
65 66 1.334869 CAAGGCAGAAGCACGACTTTT 59.665 47.619 0.00 0.00 44.61 2.27
101 102 1.251527 TTCGAGAGGCACTGTCCCTC 61.252 60.000 9.87 9.87 46.96 4.30
195 199 6.627087 TTTTCCTTCTCCATGAGATACAGT 57.373 37.500 0.00 0.00 38.56 3.55
251 255 3.487042 CGAGAAGCAAATTCATGCCTCTG 60.487 47.826 7.77 0.00 44.89 3.35
347 366 3.151912 AGAAGCAAATCAGTGCCTCTT 57.848 42.857 0.00 0.00 41.52 2.85
457 478 1.417517 TGTTGAGTCAGTCAGGCATGT 59.582 47.619 0.00 0.00 36.21 3.21
501 532 2.475371 ATTGAGACGCAGCCTTGGCT 62.475 55.000 8.56 8.56 0.00 4.75
527 559 6.667848 TCTGTGTCCTACCTCTTTATCATTCA 59.332 38.462 0.00 0.00 0.00 2.57
561 593 2.572209 TAAGGGGGTTTGTGTGTAGC 57.428 50.000 0.00 0.00 0.00 3.58
587 619 1.108727 CATGGTGGGTGTGTTGTGCT 61.109 55.000 0.00 0.00 0.00 4.40
665 697 8.103305 TCAGTTGAATGAGATTTAACTAAGGCT 58.897 33.333 6.25 0.00 44.23 4.58
684 716 5.433526 AGGCTTAGTTAAGTGACACAACAA 58.566 37.500 8.59 0.00 35.75 2.83
762 800 9.995957 AAGATCTCACGATTATAACATCTATCG 57.004 33.333 0.00 0.00 43.92 2.92
763 801 8.616942 AGATCTCACGATTATAACATCTATCGG 58.383 37.037 0.00 0.00 42.95 4.18
897 941 2.032178 GAGAATTTTCTTCGGATGCCCG 59.968 50.000 0.00 0.00 46.88 6.13
906 950 3.845259 GGATGCCCGCCGTGACTA 61.845 66.667 0.00 0.00 0.00 2.59
928 972 0.816825 ATGCAAATCCGCTCATCGCT 60.817 50.000 0.00 0.00 36.73 4.93
976 1020 1.079127 GCTTAGCGGTCAAGCTCCA 60.079 57.895 16.40 0.00 45.67 3.86
993 1037 1.440893 CAGCCAGTCTCGCATAGCT 59.559 57.895 0.00 0.00 0.00 3.32
995 1039 1.067669 CAGCCAGTCTCGCATAGCTAA 59.932 52.381 0.00 0.00 0.00 3.09
996 1040 1.067821 AGCCAGTCTCGCATAGCTAAC 59.932 52.381 0.00 0.00 0.00 2.34
1004 1048 3.004839 TCTCGCATAGCTAACTGATCCAC 59.995 47.826 0.00 0.00 0.00 4.02
1065 1109 1.660575 CAACGCAGGTTCGTCGTCT 60.661 57.895 0.00 0.00 42.46 4.18
1068 1112 2.649034 GCAGGTTCGTCGTCTCCA 59.351 61.111 0.00 0.00 0.00 3.86
1301 1363 4.832608 GATCCGGGGACACGCCAC 62.833 72.222 0.00 0.00 38.95 5.01
1342 1404 3.449227 CGTACCTCGCCAGCCAGA 61.449 66.667 0.00 0.00 0.00 3.86
1451 1525 4.473520 CAGGATCCGCGGCACCTT 62.474 66.667 30.40 18.09 0.00 3.50
1482 1556 4.477975 GTCGTCGCCGTCCTCCAG 62.478 72.222 0.00 0.00 35.01 3.86
1485 1559 4.500116 GTCGCCGTCCTCCAGCTC 62.500 72.222 0.00 0.00 0.00 4.09
1490 1564 4.838486 CGTCCTCCAGCTCGCGTC 62.838 72.222 5.77 0.00 0.00 5.19
1491 1565 4.838486 GTCCTCCAGCTCGCGTCG 62.838 72.222 5.77 0.00 0.00 5.12
1493 1567 4.838486 CCTCCAGCTCGCGTCGTC 62.838 72.222 5.77 0.00 0.00 4.20
1529 1603 4.436998 GTCCCTCGCGTCCTGGTG 62.437 72.222 5.77 0.02 0.00 4.17
1537 1611 3.625897 CGTCCTGGTGCTGGTGGA 61.626 66.667 0.00 0.00 0.00 4.02
1538 1612 2.032681 GTCCTGGTGCTGGTGGAC 59.967 66.667 0.00 0.00 41.52 4.02
1539 1613 3.625897 TCCTGGTGCTGGTGGACG 61.626 66.667 0.00 0.00 35.23 4.79
1541 1615 2.047844 CTGGTGCTGGTGGACGAG 60.048 66.667 0.00 0.00 34.61 4.18
1542 1616 4.314440 TGGTGCTGGTGGACGAGC 62.314 66.667 6.82 6.82 46.09 5.03
1836 3072 2.169327 GTGTACGCGTTTGCCGTC 59.831 61.111 20.78 0.31 39.32 4.79
1971 3228 7.663081 ACGGAGCATCATTATTATGAATCTGTT 59.337 33.333 10.95 0.40 43.67 3.16
2019 3276 6.690194 AGCTAAGCTAAATCCTTTGTGATG 57.310 37.500 0.00 0.00 36.99 3.07
2024 3281 7.472334 AAGCTAAATCCTTTGTGATGTGAAT 57.528 32.000 0.00 0.00 0.00 2.57
2063 3320 4.566004 TGGATACAGAAAAACGAGACTGG 58.434 43.478 0.00 0.00 46.17 4.00
2077 3334 3.491964 CGAGACTGGTTGAGTGTTTGGTA 60.492 47.826 0.00 0.00 33.83 3.25
2078 3335 3.805207 AGACTGGTTGAGTGTTTGGTAC 58.195 45.455 0.00 0.00 33.83 3.34
2092 3722 4.751098 TGTTTGGTACGGTGTAAGTTGATC 59.249 41.667 0.00 0.00 0.00 2.92
2120 3750 2.573340 CCAATTTGGGCTCCACGC 59.427 61.111 7.60 0.00 32.67 5.34
2139 3769 2.329379 GCAACTCTTCCGTGTCTACAG 58.671 52.381 0.00 0.00 0.00 2.74
2142 3772 1.269998 ACTCTTCCGTGTCTACAGTGC 59.730 52.381 0.00 0.00 0.00 4.40
2149 3779 3.508402 TCCGTGTCTACAGTGCTAAATGA 59.492 43.478 0.00 0.00 0.00 2.57
2154 3784 7.298122 CGTGTCTACAGTGCTAAATGATTTTT 58.702 34.615 0.00 0.00 0.00 1.94
2155 3785 8.440059 CGTGTCTACAGTGCTAAATGATTTTTA 58.560 33.333 0.00 0.00 0.00 1.52
2197 3827 3.860968 TTTTTACTCCCTCCGTTCCAA 57.139 42.857 0.00 0.00 0.00 3.53
2198 3828 3.860968 TTTTACTCCCTCCGTTCCAAA 57.139 42.857 0.00 0.00 0.00 3.28
2199 3829 4.376225 TTTTACTCCCTCCGTTCCAAAT 57.624 40.909 0.00 0.00 0.00 2.32
2200 3830 4.376225 TTTACTCCCTCCGTTCCAAATT 57.624 40.909 0.00 0.00 0.00 1.82
2201 3831 5.502089 TTTACTCCCTCCGTTCCAAATTA 57.498 39.130 0.00 0.00 0.00 1.40
2202 3832 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2203 3833 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2204 3834 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
2205 3835 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
2206 3836 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
2207 3837 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
2208 3838 3.124636 CCTCCGTTCCAAATTACTTGTCG 59.875 47.826 0.00 0.00 32.65 4.35
2209 3839 2.481185 TCCGTTCCAAATTACTTGTCGC 59.519 45.455 0.00 0.00 32.65 5.19
2210 3840 2.224549 CCGTTCCAAATTACTTGTCGCA 59.775 45.455 0.00 0.00 32.65 5.10
2211 3841 3.304123 CCGTTCCAAATTACTTGTCGCAA 60.304 43.478 0.00 0.00 32.65 4.85
2212 3842 4.283678 CGTTCCAAATTACTTGTCGCAAA 58.716 39.130 0.00 0.00 32.65 3.68
2213 3843 4.915085 CGTTCCAAATTACTTGTCGCAAAT 59.085 37.500 0.00 0.00 32.65 2.32
2214 3844 6.081049 CGTTCCAAATTACTTGTCGCAAATA 58.919 36.000 0.00 0.00 32.65 1.40
2215 3845 6.745450 CGTTCCAAATTACTTGTCGCAAATAT 59.255 34.615 0.00 0.00 32.65 1.28
2216 3846 7.253288 CGTTCCAAATTACTTGTCGCAAATATG 60.253 37.037 0.00 0.00 32.65 1.78
2217 3847 6.559810 TCCAAATTACTTGTCGCAAATATGG 58.440 36.000 0.00 0.00 32.65 2.74
2218 3848 6.375736 TCCAAATTACTTGTCGCAAATATGGA 59.624 34.615 0.00 0.00 32.65 3.41
2219 3849 7.068103 TCCAAATTACTTGTCGCAAATATGGAT 59.932 33.333 0.00 0.00 32.65 3.41
2220 3850 7.167968 CCAAATTACTTGTCGCAAATATGGATG 59.832 37.037 0.00 0.00 32.65 3.51
2221 3851 6.942532 ATTACTTGTCGCAAATATGGATGT 57.057 33.333 0.00 0.00 0.00 3.06
2222 3852 8.445275 AATTACTTGTCGCAAATATGGATGTA 57.555 30.769 0.00 0.00 0.00 2.29
2223 3853 8.621532 ATTACTTGTCGCAAATATGGATGTAT 57.378 30.769 0.00 0.00 0.00 2.29
2224 3854 6.545504 ACTTGTCGCAAATATGGATGTATC 57.454 37.500 0.00 0.00 0.00 2.24
2225 3855 6.291377 ACTTGTCGCAAATATGGATGTATCT 58.709 36.000 0.00 0.00 0.00 1.98
2226 3856 7.441836 ACTTGTCGCAAATATGGATGTATCTA 58.558 34.615 0.00 0.00 0.00 1.98
2227 3857 7.600375 ACTTGTCGCAAATATGGATGTATCTAG 59.400 37.037 0.00 0.00 0.00 2.43
2228 3858 7.227049 TGTCGCAAATATGGATGTATCTAGA 57.773 36.000 0.00 0.00 0.00 2.43
2229 3859 7.840931 TGTCGCAAATATGGATGTATCTAGAT 58.159 34.615 10.73 10.73 0.00 1.98
2230 3860 8.966868 TGTCGCAAATATGGATGTATCTAGATA 58.033 33.333 8.44 8.44 0.00 1.98
2231 3861 9.239002 GTCGCAAATATGGATGTATCTAGATAC 57.761 37.037 28.75 28.75 42.95 2.24
2261 3891 7.706281 AGTTCTAGATACATCAATTTCTGCG 57.294 36.000 0.00 0.00 0.00 5.18
2262 3892 7.492524 AGTTCTAGATACATCAATTTCTGCGA 58.507 34.615 0.00 0.00 0.00 5.10
2263 3893 7.436673 AGTTCTAGATACATCAATTTCTGCGAC 59.563 37.037 0.00 0.00 0.00 5.19
2264 3894 5.915196 TCTAGATACATCAATTTCTGCGACG 59.085 40.000 0.00 0.00 0.00 5.12
2265 3895 4.682787 AGATACATCAATTTCTGCGACGA 58.317 39.130 0.00 0.00 0.00 4.20
2266 3896 4.742167 AGATACATCAATTTCTGCGACGAG 59.258 41.667 0.00 0.00 0.00 4.18
2267 3897 2.688507 ACATCAATTTCTGCGACGAGT 58.311 42.857 0.00 0.00 0.00 4.18
2268 3898 3.845178 ACATCAATTTCTGCGACGAGTA 58.155 40.909 0.00 0.00 0.00 2.59
2269 3899 4.242475 ACATCAATTTCTGCGACGAGTAA 58.758 39.130 0.00 0.00 0.00 2.24
2270 3900 4.870426 ACATCAATTTCTGCGACGAGTAAT 59.130 37.500 0.00 0.00 0.00 1.89
2271 3901 5.351465 ACATCAATTTCTGCGACGAGTAATT 59.649 36.000 0.00 2.98 0.00 1.40
2272 3902 5.856126 TCAATTTCTGCGACGAGTAATTT 57.144 34.783 0.00 0.00 0.00 1.82
2273 3903 5.617609 TCAATTTCTGCGACGAGTAATTTG 58.382 37.500 0.00 2.50 0.00 2.32
2274 3904 5.407084 TCAATTTCTGCGACGAGTAATTTGA 59.593 36.000 0.00 4.70 0.00 2.69
2275 3905 5.856126 ATTTCTGCGACGAGTAATTTGAA 57.144 34.783 0.00 0.00 0.00 2.69
2276 3906 5.660629 TTTCTGCGACGAGTAATTTGAAA 57.339 34.783 0.00 0.00 0.00 2.69
2277 3907 4.640805 TCTGCGACGAGTAATTTGAAAC 57.359 40.909 0.00 0.00 0.00 2.78
2278 3908 3.120616 TCTGCGACGAGTAATTTGAAACG 59.879 43.478 0.00 0.00 0.00 3.60
2279 3909 2.156117 TGCGACGAGTAATTTGAAACGG 59.844 45.455 0.00 0.00 0.00 4.44
2280 3910 2.409378 GCGACGAGTAATTTGAAACGGA 59.591 45.455 0.00 0.00 0.00 4.69
2281 3911 3.481467 GCGACGAGTAATTTGAAACGGAG 60.481 47.826 0.00 0.00 0.00 4.63
2282 3912 3.916172 CGACGAGTAATTTGAAACGGAGA 59.084 43.478 0.00 0.00 0.00 3.71
2283 3913 4.030306 CGACGAGTAATTTGAAACGGAGAG 59.970 45.833 0.00 0.00 0.00 3.20
2284 3914 5.130292 ACGAGTAATTTGAAACGGAGAGA 57.870 39.130 0.00 0.00 0.00 3.10
2285 3915 5.162075 ACGAGTAATTTGAAACGGAGAGAG 58.838 41.667 0.00 0.00 0.00 3.20
2286 3916 5.162075 CGAGTAATTTGAAACGGAGAGAGT 58.838 41.667 0.00 0.00 0.00 3.24
2287 3917 6.072286 ACGAGTAATTTGAAACGGAGAGAGTA 60.072 38.462 0.00 0.00 0.00 2.59
2288 3918 6.250951 CGAGTAATTTGAAACGGAGAGAGTAC 59.749 42.308 0.00 0.00 0.00 2.73
2322 3952 7.881775 ACAACTCCATTAAAGAAACTGAGTT 57.118 32.000 0.00 0.00 39.81 3.01
2323 3953 8.293699 ACAACTCCATTAAAGAAACTGAGTTT 57.706 30.769 10.82 10.82 38.37 2.66
2326 3956 9.628500 AACTCCATTAAAGAAACTGAGTTTAGT 57.372 29.630 11.01 4.67 37.72 2.24
2335 3965 8.967552 AAGAAACTGAGTTTAGTACTACATCG 57.032 34.615 11.01 1.55 37.17 3.84
2339 3969 8.739649 AACTGAGTTTAGTACTACATCGAAAC 57.260 34.615 0.91 5.39 37.17 2.78
2342 3972 8.683550 TGAGTTTAGTACTACATCGAAACATG 57.316 34.615 15.52 0.00 37.17 3.21
2367 3997 9.052759 TGGAGACAGAAAGTAAAGTGAATAAAC 57.947 33.333 0.00 0.00 35.01 2.01
2386 4029 9.229784 GAATAAACAATAGAGTGCAACATCATG 57.770 33.333 0.00 0.00 41.43 3.07
2407 4050 2.033049 GGCTAACATTGCAGCATCTCTG 59.967 50.000 0.00 0.00 45.62 3.35
2415 4058 3.449528 TGCAGCATCTCTGACATAGTC 57.550 47.619 0.00 0.00 45.72 2.59
2416 4059 2.223665 TGCAGCATCTCTGACATAGTCG 60.224 50.000 0.00 0.00 45.72 4.18
2417 4060 2.861750 GCAGCATCTCTGACATAGTCGG 60.862 54.545 0.00 0.00 45.72 4.79
2418 4061 2.620585 CAGCATCTCTGACATAGTCGGA 59.379 50.000 8.27 8.27 45.72 4.55
2422 4065 3.905331 TCTGACATAGTCGGAGCCT 57.095 52.632 4.64 0.00 42.21 4.58
2448 4091 3.508793 AGGTTCATCACTCAGCAAAATGG 59.491 43.478 0.00 0.00 0.00 3.16
2487 4130 3.555956 ACGCAGAACACTACAGAAAACAG 59.444 43.478 0.00 0.00 0.00 3.16
2500 4143 1.526464 GAAAACAGGGCATGCAAAACG 59.474 47.619 21.36 5.16 0.00 3.60
2513 4156 4.273005 TGCAAAACGAAACTTCAGAGTC 57.727 40.909 0.00 0.00 34.21 3.36
2525 4168 0.596600 TCAGAGTCACGACCAAACGC 60.597 55.000 0.00 0.00 36.70 4.84
2527 4170 1.659335 GAGTCACGACCAAACGCGA 60.659 57.895 15.93 0.00 36.70 5.87
2535 4178 4.741781 CCAAACGCGAGCAAGCCG 62.742 66.667 15.93 0.00 0.00 5.52
2567 4210 3.504134 CGGGTACAACAATCATCCAACAA 59.496 43.478 0.00 0.00 0.00 2.83
2603 4246 2.677228 CCCATCCTTTCGCCTGGT 59.323 61.111 0.00 0.00 0.00 4.00
2612 4255 1.104577 TTTCGCCTGGTCAAACACCC 61.105 55.000 0.00 0.00 46.18 4.61
2640 4283 2.811317 CGCCGTGAGTCTTCTGGC 60.811 66.667 5.71 5.71 40.18 4.85
2681 4324 2.064014 GCACATTTTCCTTCTGCAAGC 58.936 47.619 0.00 0.00 0.00 4.01
2686 4329 0.179004 TTTCCTTCTGCAAGCCGGAA 60.179 50.000 5.05 3.18 39.24 4.30
2688 4331 1.600636 CCTTCTGCAAGCCGGAACA 60.601 57.895 5.05 0.00 35.08 3.18
2689 4332 1.172180 CCTTCTGCAAGCCGGAACAA 61.172 55.000 5.05 0.00 35.08 2.83
2700 4343 5.217393 CAAGCCGGAACAATCATCAATATG 58.783 41.667 5.05 0.00 0.00 1.78
2702 4345 3.612479 GCCGGAACAATCATCAATATGCC 60.612 47.826 5.05 0.00 32.76 4.40
2726 4369 7.570140 GCCGACATATTCAATGAATGACACTAG 60.570 40.741 17.93 3.62 37.92 2.57
2727 4370 7.439356 CCGACATATTCAATGAATGACACTAGT 59.561 37.037 17.93 6.19 37.92 2.57
2728 4371 9.463443 CGACATATTCAATGAATGACACTAGTA 57.537 33.333 17.93 0.00 37.92 1.82
2748 4391 2.498167 AGCAATATCATTCGGGCACTC 58.502 47.619 0.00 0.00 0.00 3.51
2752 4395 4.555511 GCAATATCATTCGGGCACTCTTTC 60.556 45.833 0.00 0.00 0.00 2.62
2758 4404 1.878953 TCGGGCACTCTTTCTGAAAC 58.121 50.000 0.00 0.00 0.00 2.78
2762 4408 1.264288 GGCACTCTTTCTGAAACCACG 59.736 52.381 0.00 0.00 0.00 4.94
2763 4409 1.940613 GCACTCTTTCTGAAACCACGT 59.059 47.619 0.00 0.00 0.00 4.49
2778 4426 3.078837 ACCACGTTTTGTTGTGTCTTCT 58.921 40.909 0.00 0.00 34.28 2.85
2787 4435 2.027192 TGTTGTGTCTTCTGGATAGCCC 60.027 50.000 0.00 0.00 0.00 5.19
2797 4445 7.017551 TGTCTTCTGGATAGCCCATATAACATT 59.982 37.037 0.00 0.00 45.57 2.71
2801 4449 6.673978 TCTGGATAGCCCATATAACATTAGCT 59.326 38.462 0.00 0.00 45.57 3.32
2802 4450 7.844269 TCTGGATAGCCCATATAACATTAGCTA 59.156 37.037 0.00 0.00 45.57 3.32
2810 4458 6.069673 CCCATATAACATTAGCTATCCCCACA 60.070 42.308 0.00 0.00 0.00 4.17
2811 4459 7.050377 CCATATAACATTAGCTATCCCCACAG 58.950 42.308 0.00 0.00 0.00 3.66
2814 4462 2.509548 ACATTAGCTATCCCCACAGCAA 59.490 45.455 0.00 0.00 40.36 3.91
2816 4464 3.951563 TTAGCTATCCCCACAGCAATT 57.048 42.857 0.00 0.00 40.36 2.32
2817 4465 2.062971 AGCTATCCCCACAGCAATTG 57.937 50.000 0.00 0.00 40.36 2.32
2818 4466 1.035139 GCTATCCCCACAGCAATTGG 58.965 55.000 7.72 0.00 37.73 3.16
2819 4467 1.035139 CTATCCCCACAGCAATTGGC 58.965 55.000 7.72 0.00 45.30 4.52
2831 4479 3.391506 GCAATTGGCTTCCTTCTGTTT 57.608 42.857 7.72 0.00 40.25 2.83
2832 4480 3.320626 GCAATTGGCTTCCTTCTGTTTC 58.679 45.455 7.72 0.00 40.25 2.78
2833 4481 3.006217 GCAATTGGCTTCCTTCTGTTTCT 59.994 43.478 7.72 0.00 40.25 2.52
2834 4482 4.218417 GCAATTGGCTTCCTTCTGTTTCTA 59.782 41.667 7.72 0.00 40.25 2.10
2836 4484 4.974645 TTGGCTTCCTTCTGTTTCTAGA 57.025 40.909 0.00 0.00 0.00 2.43
2861 4509 4.708726 ACTTTAGATCATTGCCAAGCAC 57.291 40.909 0.00 0.00 38.71 4.40
2867 4515 0.895100 TCATTGCCAAGCACTGACCC 60.895 55.000 5.62 0.00 41.87 4.46
2877 4525 0.393537 GCACTGACCCAAGCTAGCAT 60.394 55.000 18.83 0.65 0.00 3.79
2905 4553 7.170658 GGTTGATGCAACTTTAAAAGTGCATTA 59.829 33.333 26.74 22.70 46.36 1.90
2917 4565 4.534647 AAGTGCATTATACAATCCCCCA 57.465 40.909 0.00 0.00 0.00 4.96
2938 4586 4.160439 CCAGATGAACCTAGCTACTGAACA 59.840 45.833 6.80 0.00 0.00 3.18
2942 4590 1.183549 ACCTAGCTACTGAACACCCG 58.816 55.000 0.00 0.00 0.00 5.28
2948 4596 3.751518 AGCTACTGAACACCCGAAAAAT 58.248 40.909 0.00 0.00 0.00 1.82
2958 4606 4.007659 ACACCCGAAAAATAGATGGTCAC 58.992 43.478 0.00 0.00 0.00 3.67
2969 4617 9.566432 AAAAATAGATGGTCACTAGATTCATCC 57.434 33.333 0.00 0.00 37.69 3.51
2972 4620 4.592351 AGATGGTCACTAGATTCATCCTGG 59.408 45.833 0.00 0.00 37.69 4.45
2977 4625 5.598830 GGTCACTAGATTCATCCTGGAACTA 59.401 44.000 0.00 0.00 0.00 2.24
2994 4642 3.451402 ACTATTTTCTCCAACCCACCC 57.549 47.619 0.00 0.00 0.00 4.61
2995 4643 2.719705 ACTATTTTCTCCAACCCACCCA 59.280 45.455 0.00 0.00 0.00 4.51
2996 4644 2.009681 ATTTTCTCCAACCCACCCAC 57.990 50.000 0.00 0.00 0.00 4.61
2997 4645 0.631753 TTTTCTCCAACCCACCCACA 59.368 50.000 0.00 0.00 0.00 4.17
3048 4696 4.218417 GCTTAAGAACCAGCCATGAGAAAA 59.782 41.667 6.67 0.00 0.00 2.29
3059 4707 6.700081 CCAGCCATGAGAAAACAATAATCATG 59.300 38.462 0.00 6.52 44.33 3.07
3065 4713 7.395190 TGAGAAAACAATAATCATGGGTGAG 57.605 36.000 0.00 0.00 37.87 3.51
3070 4718 7.814264 AAACAATAATCATGGGTGAGATCTC 57.186 36.000 16.21 16.21 37.87 2.75
3105 4753 0.179004 ACGACAACCATCAAAGGGCA 60.179 50.000 0.00 0.00 0.00 5.36
3118 4766 5.389859 TCAAAGGGCAAGTGTGAATAATG 57.610 39.130 0.00 0.00 0.00 1.90
3225 4876 5.551305 TCTGACACAAGATCCTTCAAAGA 57.449 39.130 0.00 0.00 0.00 2.52
3233 4884 7.939039 ACACAAGATCCTTCAAAGAAACTCATA 59.061 33.333 0.00 0.00 0.00 2.15
3234 4885 8.954350 CACAAGATCCTTCAAAGAAACTCATAT 58.046 33.333 0.00 0.00 0.00 1.78
3250 4901 7.939784 AACTCATATTTCTAGGAAAACACCC 57.060 36.000 0.00 0.00 0.00 4.61
3259 4910 1.710809 AGGAAAACACCCCACATAGCT 59.289 47.619 0.00 0.00 0.00 3.32
3311 4962 9.212641 CACTCATGATTACCTTATCAACCATAG 57.787 37.037 0.00 0.00 38.01 2.23
3313 4964 9.212641 CTCATGATTACCTTATCAACCATAGTG 57.787 37.037 0.00 0.00 38.01 2.74
3318 4969 8.732746 ATTACCTTATCAACCATAGTGTTCAC 57.267 34.615 0.00 0.00 0.00 3.18
3319 4970 5.175859 ACCTTATCAACCATAGTGTTCACG 58.824 41.667 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 7.291411 TGGATTTTCTTTACCCATTTTTCGA 57.709 32.000 0.00 0.00 0.00 3.71
37 38 2.560105 GTGCTTCTGCCTTGGATTTTCT 59.440 45.455 0.00 0.00 38.71 2.52
38 39 2.669391 CGTGCTTCTGCCTTGGATTTTC 60.669 50.000 0.00 0.00 38.71 2.29
101 102 0.664761 CACATATTTGCTCCCGCCAG 59.335 55.000 0.00 0.00 34.43 4.85
175 179 5.026121 ACAACTGTATCTCATGGAGAAGGA 58.974 41.667 0.00 0.00 42.27 3.36
180 184 3.118482 AGGCACAACTGTATCTCATGGAG 60.118 47.826 0.00 0.00 0.00 3.86
195 199 4.887071 AGTTTGTTTCTACATGAGGCACAA 59.113 37.500 0.00 0.00 33.44 3.33
347 366 5.514274 AAAACTCATTTTTCTCTTCCGCA 57.486 34.783 0.00 0.00 34.19 5.69
428 449 5.126396 TGACTGACTCAACACATACTCTG 57.874 43.478 0.00 0.00 0.00 3.35
429 450 4.219507 CCTGACTGACTCAACACATACTCT 59.780 45.833 0.00 0.00 0.00 3.24
457 478 7.487484 TCAATGTTGAAGCATGAACAAAACTA 58.513 30.769 0.00 0.00 35.76 2.24
501 532 7.180229 TGAATGATAAAGAGGTAGGACACAGAA 59.820 37.037 0.00 0.00 0.00 3.02
527 559 1.417890 CCCTTATCGGTCTCAAGCCAT 59.582 52.381 0.00 0.00 0.00 4.40
561 593 1.347707 ACACACCCACCATGACTACAG 59.652 52.381 0.00 0.00 0.00 2.74
746 778 4.733887 CGACCGCCGATAGATGTTATAATC 59.266 45.833 0.00 0.00 41.76 1.75
762 800 1.062148 GCTAAATTTCAGTCGACCGCC 59.938 52.381 13.01 0.00 0.00 6.13
763 801 1.730064 TGCTAAATTTCAGTCGACCGC 59.270 47.619 13.01 2.13 0.00 5.68
906 950 0.940126 GATGAGCGGATTTGCATCGT 59.060 50.000 0.00 0.00 37.31 3.73
976 1020 1.067821 GTTAGCTATGCGAGACTGGCT 59.932 52.381 10.98 0.00 0.00 4.75
993 1037 2.711009 GGATGGATGGGTGGATCAGTTA 59.289 50.000 0.00 0.00 0.00 2.24
995 1039 1.143813 GGATGGATGGGTGGATCAGT 58.856 55.000 0.00 0.00 0.00 3.41
996 1040 1.142936 TGGATGGATGGGTGGATCAG 58.857 55.000 0.00 0.00 0.00 2.90
1004 1048 3.428532 GAGGAATTGATGGATGGATGGG 58.571 50.000 0.00 0.00 0.00 4.00
1065 1109 3.858868 GACGAAGCTGGTGCGTGGA 62.859 63.158 18.80 0.00 45.42 4.02
1118 1162 2.615262 GAAGGCGGACGCGAAGATCT 62.615 60.000 15.93 1.14 43.06 2.75
1120 1164 2.202756 GAAGGCGGACGCGAAGAT 60.203 61.111 15.93 0.00 43.06 2.40
1248 1292 1.298190 CGCGTAGAAGTCGTAGCCC 60.298 63.158 0.00 0.00 0.00 5.19
1301 1363 0.383949 GTAGAGGAGGAGCAGCTTCG 59.616 60.000 0.00 0.00 0.00 3.79
1434 1508 4.473520 AAGGTGCCGCGGATCCTG 62.474 66.667 31.76 7.78 0.00 3.86
1473 1547 4.838486 GACGCGAGCTGGAGGACG 62.838 72.222 15.93 0.00 0.00 4.79
1477 1551 4.838486 GGACGACGCGAGCTGGAG 62.838 72.222 15.93 0.00 0.00 3.86
1512 1586 4.436998 CACCAGGACGCGAGGGAC 62.437 72.222 15.93 0.00 0.00 4.46
1520 1594 3.625897 TCCACCAGCACCAGGACG 61.626 66.667 0.00 0.00 0.00 4.79
1521 1595 2.032681 GTCCACCAGCACCAGGAC 59.967 66.667 0.00 0.00 43.18 3.85
1523 1597 3.596066 CTCGTCCACCAGCACCAGG 62.596 68.421 0.00 0.00 0.00 4.45
1524 1598 2.047844 CTCGTCCACCAGCACCAG 60.048 66.667 0.00 0.00 0.00 4.00
1525 1599 4.314440 GCTCGTCCACCAGCACCA 62.314 66.667 0.00 0.00 35.56 4.17
1571 1645 2.179018 CAAAAGATGCCACGGCGG 59.821 61.111 13.24 0.00 45.51 6.13
1572 1646 1.442520 CACAAAAGATGCCACGGCG 60.443 57.895 4.80 4.80 45.51 6.46
1573 1647 0.387239 GACACAAAAGATGCCACGGC 60.387 55.000 0.00 0.00 42.35 5.68
1574 1648 0.950836 TGACACAAAAGATGCCACGG 59.049 50.000 0.00 0.00 0.00 4.94
1575 1649 1.069022 CCTGACACAAAAGATGCCACG 60.069 52.381 0.00 0.00 0.00 4.94
1576 1650 1.336240 GCCTGACACAAAAGATGCCAC 60.336 52.381 0.00 0.00 0.00 5.01
1578 1652 1.251251 AGCCTGACACAAAAGATGCC 58.749 50.000 0.00 0.00 0.00 4.40
1579 1653 2.159653 CGTAGCCTGACACAAAAGATGC 60.160 50.000 0.00 0.00 0.00 3.91
1583 1657 1.069906 GCACGTAGCCTGACACAAAAG 60.070 52.381 0.00 0.00 37.23 2.27
1585 1659 2.612200 GCACGTAGCCTGACACAAA 58.388 52.632 0.00 0.00 37.23 2.83
1586 1660 4.354155 GCACGTAGCCTGACACAA 57.646 55.556 0.00 0.00 37.23 3.33
1836 3072 1.790387 GCCGCTCTGCAAACAGTAG 59.210 57.895 0.00 0.00 44.77 2.57
1971 3228 3.326836 TGTTTCATCGTCAGTGGCATA 57.673 42.857 0.00 0.00 0.00 3.14
2048 3305 3.871594 CACTCAACCAGTCTCGTTTTTCT 59.128 43.478 0.00 0.00 30.26 2.52
2063 3320 2.282407 ACACCGTACCAAACACTCAAC 58.718 47.619 0.00 0.00 0.00 3.18
2077 3334 3.057104 TCATGTCGATCAACTTACACCGT 60.057 43.478 0.00 0.00 0.00 4.83
2078 3335 3.507786 TCATGTCGATCAACTTACACCG 58.492 45.455 0.00 0.00 0.00 4.94
2092 3722 1.135315 CCCAAATTGGCACTCATGTCG 60.135 52.381 6.48 0.00 35.79 4.35
2120 3750 3.309388 CACTGTAGACACGGAAGAGTTG 58.691 50.000 0.00 0.00 34.22 3.16
2122 3752 1.269998 GCACTGTAGACACGGAAGAGT 59.730 52.381 0.00 0.00 37.72 3.24
2178 3808 3.860968 TTTGGAACGGAGGGAGTAAAA 57.139 42.857 0.00 0.00 0.00 1.52
2179 3809 4.376225 AATTTGGAACGGAGGGAGTAAA 57.624 40.909 0.00 0.00 0.00 2.01
2180 3810 4.533311 AGTAATTTGGAACGGAGGGAGTAA 59.467 41.667 0.00 0.00 0.00 2.24
2181 3811 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
2182 3812 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
2183 3813 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
2184 3814 3.073356 ACAAGTAATTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 41.25 4.20
2185 3815 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
2186 3816 3.124636 CGACAAGTAATTTGGAACGGAGG 59.875 47.826 0.00 0.00 41.25 4.30
2187 3817 3.424433 GCGACAAGTAATTTGGAACGGAG 60.424 47.826 0.00 0.00 41.25 4.63
2188 3818 2.481185 GCGACAAGTAATTTGGAACGGA 59.519 45.455 0.00 0.00 41.25 4.69
2189 3819 2.224549 TGCGACAAGTAATTTGGAACGG 59.775 45.455 0.00 0.00 41.25 4.44
2190 3820 3.529634 TGCGACAAGTAATTTGGAACG 57.470 42.857 0.00 0.00 41.25 3.95
2191 3821 7.009174 CCATATTTGCGACAAGTAATTTGGAAC 59.991 37.037 0.00 0.00 41.25 3.62
2192 3822 7.032580 CCATATTTGCGACAAGTAATTTGGAA 58.967 34.615 0.00 0.00 41.25 3.53
2193 3823 6.375736 TCCATATTTGCGACAAGTAATTTGGA 59.624 34.615 0.00 0.00 41.25 3.53
2194 3824 6.559810 TCCATATTTGCGACAAGTAATTTGG 58.440 36.000 0.00 0.00 41.25 3.28
2195 3825 7.701924 ACATCCATATTTGCGACAAGTAATTTG 59.298 33.333 0.00 0.00 42.68 2.32
2196 3826 7.771183 ACATCCATATTTGCGACAAGTAATTT 58.229 30.769 0.00 0.00 0.00 1.82
2197 3827 7.333528 ACATCCATATTTGCGACAAGTAATT 57.666 32.000 0.00 0.00 0.00 1.40
2198 3828 6.942532 ACATCCATATTTGCGACAAGTAAT 57.057 33.333 0.00 0.00 0.00 1.89
2199 3829 7.931407 AGATACATCCATATTTGCGACAAGTAA 59.069 33.333 0.00 0.00 0.00 2.24
2200 3830 7.441836 AGATACATCCATATTTGCGACAAGTA 58.558 34.615 0.00 0.00 0.00 2.24
2201 3831 6.291377 AGATACATCCATATTTGCGACAAGT 58.709 36.000 0.00 0.00 0.00 3.16
2202 3832 6.791887 AGATACATCCATATTTGCGACAAG 57.208 37.500 0.00 0.00 0.00 3.16
2203 3833 7.666623 TCTAGATACATCCATATTTGCGACAA 58.333 34.615 0.00 0.00 0.00 3.18
2204 3834 7.227049 TCTAGATACATCCATATTTGCGACA 57.773 36.000 0.00 0.00 0.00 4.35
2205 3835 9.239002 GTATCTAGATACATCCATATTTGCGAC 57.761 37.037 29.91 6.35 42.37 5.19
2206 3836 8.966868 TGTATCTAGATACATCCATATTTGCGA 58.033 33.333 32.50 12.04 46.11 5.10
2235 3865 9.249457 CGCAGAAATTGATGTATCTAGAACTAA 57.751 33.333 0.00 0.00 0.00 2.24
2236 3866 8.630037 TCGCAGAAATTGATGTATCTAGAACTA 58.370 33.333 0.00 0.00 0.00 2.24
2237 3867 7.436673 GTCGCAGAAATTGATGTATCTAGAACT 59.563 37.037 0.00 0.00 39.69 3.01
2238 3868 7.559845 GTCGCAGAAATTGATGTATCTAGAAC 58.440 38.462 0.00 0.00 39.69 3.01
2239 3869 6.417930 CGTCGCAGAAATTGATGTATCTAGAA 59.582 38.462 0.00 0.00 39.69 2.10
2240 3870 5.915196 CGTCGCAGAAATTGATGTATCTAGA 59.085 40.000 0.00 0.00 39.69 2.43
2241 3871 5.915196 TCGTCGCAGAAATTGATGTATCTAG 59.085 40.000 0.00 0.00 39.69 2.43
2242 3872 5.827666 TCGTCGCAGAAATTGATGTATCTA 58.172 37.500 0.00 0.00 39.69 1.98
2243 3873 4.682787 TCGTCGCAGAAATTGATGTATCT 58.317 39.130 0.00 0.00 39.69 1.98
2244 3874 4.504461 ACTCGTCGCAGAAATTGATGTATC 59.496 41.667 0.00 0.00 39.69 2.24
2245 3875 4.433615 ACTCGTCGCAGAAATTGATGTAT 58.566 39.130 0.00 0.00 39.69 2.29
2246 3876 3.845178 ACTCGTCGCAGAAATTGATGTA 58.155 40.909 0.00 0.00 39.69 2.29
2247 3877 2.688507 ACTCGTCGCAGAAATTGATGT 58.311 42.857 0.00 0.00 39.69 3.06
2248 3878 4.840401 TTACTCGTCGCAGAAATTGATG 57.160 40.909 0.00 0.00 39.69 3.07
2249 3879 6.092122 TCAAATTACTCGTCGCAGAAATTGAT 59.908 34.615 0.00 0.00 39.69 2.57
2250 3880 5.407084 TCAAATTACTCGTCGCAGAAATTGA 59.593 36.000 0.00 0.00 39.69 2.57
2251 3881 5.617609 TCAAATTACTCGTCGCAGAAATTG 58.382 37.500 0.00 0.00 39.69 2.32
2252 3882 5.856126 TCAAATTACTCGTCGCAGAAATT 57.144 34.783 0.00 0.00 39.69 1.82
2253 3883 5.856126 TTCAAATTACTCGTCGCAGAAAT 57.144 34.783 0.00 0.00 39.69 2.17
2254 3884 5.437263 GTTTCAAATTACTCGTCGCAGAAA 58.563 37.500 0.00 0.00 39.69 2.52
2255 3885 4.375606 CGTTTCAAATTACTCGTCGCAGAA 60.376 41.667 0.00 0.00 39.69 3.02
2256 3886 3.120616 CGTTTCAAATTACTCGTCGCAGA 59.879 43.478 0.00 0.00 0.00 4.26
2257 3887 3.395671 CGTTTCAAATTACTCGTCGCAG 58.604 45.455 0.00 0.00 0.00 5.18
2258 3888 2.156117 CCGTTTCAAATTACTCGTCGCA 59.844 45.455 0.00 0.00 0.00 5.10
2259 3889 2.409378 TCCGTTTCAAATTACTCGTCGC 59.591 45.455 0.00 0.00 0.00 5.19
2260 3890 3.916172 TCTCCGTTTCAAATTACTCGTCG 59.084 43.478 0.00 0.00 0.00 5.12
2261 3891 5.159209 TCTCTCCGTTTCAAATTACTCGTC 58.841 41.667 0.00 0.00 0.00 4.20
2262 3892 5.130292 TCTCTCCGTTTCAAATTACTCGT 57.870 39.130 0.00 0.00 0.00 4.18
2263 3893 5.162075 ACTCTCTCCGTTTCAAATTACTCG 58.838 41.667 0.00 0.00 0.00 4.18
2264 3894 7.314393 AGTACTCTCTCCGTTTCAAATTACTC 58.686 38.462 0.00 0.00 0.00 2.59
2265 3895 7.229581 AGTACTCTCTCCGTTTCAAATTACT 57.770 36.000 0.00 0.00 0.00 2.24
2266 3896 7.886405 AAGTACTCTCTCCGTTTCAAATTAC 57.114 36.000 0.00 0.00 0.00 1.89
2267 3897 8.897872 AAAAGTACTCTCTCCGTTTCAAATTA 57.102 30.769 0.00 0.00 0.00 1.40
2268 3898 7.803279 AAAAGTACTCTCTCCGTTTCAAATT 57.197 32.000 0.00 0.00 0.00 1.82
2269 3899 7.803279 AAAAAGTACTCTCTCCGTTTCAAAT 57.197 32.000 0.00 0.00 0.00 2.32
2295 3925 8.406297 ACTCAGTTTCTTTAATGGAGTTGTTTC 58.594 33.333 0.00 0.00 31.77 2.78
2309 3939 9.408069 CGATGTAGTACTAAACTCAGTTTCTTT 57.592 33.333 5.92 0.00 39.80 2.52
2316 3946 8.799091 CATGTTTCGATGTAGTACTAAACTCAG 58.201 37.037 3.61 0.00 39.80 3.35
2322 3952 7.121611 TGTCTCCATGTTTCGATGTAGTACTAA 59.878 37.037 3.61 0.00 0.00 2.24
2323 3953 6.600427 TGTCTCCATGTTTCGATGTAGTACTA 59.400 38.462 0.00 0.00 0.00 1.82
2326 3956 5.650703 TCTGTCTCCATGTTTCGATGTAGTA 59.349 40.000 0.00 0.00 0.00 1.82
2327 3957 4.462834 TCTGTCTCCATGTTTCGATGTAGT 59.537 41.667 0.00 0.00 0.00 2.73
2328 3958 4.998788 TCTGTCTCCATGTTTCGATGTAG 58.001 43.478 0.00 0.00 0.00 2.74
2335 3965 7.226720 TCACTTTACTTTCTGTCTCCATGTTTC 59.773 37.037 0.00 0.00 0.00 2.78
2339 3969 7.678947 ATTCACTTTACTTTCTGTCTCCATG 57.321 36.000 0.00 0.00 0.00 3.66
2342 3972 9.052759 TGTTTATTCACTTTACTTTCTGTCTCC 57.947 33.333 0.00 0.00 0.00 3.71
2367 3997 3.630769 AGCCATGATGTTGCACTCTATTG 59.369 43.478 0.00 0.00 0.00 1.90
2369 3999 3.572632 AGCCATGATGTTGCACTCTAT 57.427 42.857 0.00 0.00 0.00 1.98
2374 4004 3.788333 ATGTTAGCCATGATGTTGCAC 57.212 42.857 0.00 0.00 30.69 4.57
2379 4022 2.100252 GCTGCAATGTTAGCCATGATGT 59.900 45.455 0.00 0.00 32.82 3.06
2386 4029 2.033049 CAGAGATGCTGCAATGTTAGCC 59.967 50.000 6.36 0.00 39.15 3.93
2407 4050 0.818445 TCCGAGGCTCCGACTATGTC 60.818 60.000 9.32 0.00 0.00 3.06
2415 4058 2.356818 GATGAACCTCCGAGGCTCCG 62.357 65.000 14.86 2.21 39.63 4.63
2416 4059 1.330655 TGATGAACCTCCGAGGCTCC 61.331 60.000 14.86 4.51 39.63 4.70
2417 4060 0.179097 GTGATGAACCTCCGAGGCTC 60.179 60.000 14.86 12.50 39.63 4.70
2418 4061 0.616111 AGTGATGAACCTCCGAGGCT 60.616 55.000 14.86 1.38 39.63 4.58
2419 4062 0.179097 GAGTGATGAACCTCCGAGGC 60.179 60.000 14.86 0.00 39.63 4.70
2420 4063 1.135915 CTGAGTGATGAACCTCCGAGG 59.864 57.143 13.31 13.31 42.49 4.63
2421 4064 1.470632 GCTGAGTGATGAACCTCCGAG 60.471 57.143 0.00 0.00 0.00 4.63
2422 4065 0.532573 GCTGAGTGATGAACCTCCGA 59.467 55.000 0.00 0.00 0.00 4.55
2448 4091 1.002366 CGTAGGCAATCTGAGTGTGC 58.998 55.000 6.98 4.78 37.55 4.57
2463 4106 4.743151 TGTTTTCTGTAGTGTTCTGCGTAG 59.257 41.667 0.00 0.00 0.00 3.51
2466 4109 3.059597 CCTGTTTTCTGTAGTGTTCTGCG 60.060 47.826 0.00 0.00 0.00 5.18
2487 4130 1.792367 GAAGTTTCGTTTTGCATGCCC 59.208 47.619 16.68 0.00 0.00 5.36
2500 4143 3.093717 TGGTCGTGACTCTGAAGTTTC 57.906 47.619 0.00 0.00 35.28 2.78
2513 4156 2.748546 CTTGCTCGCGTTTGGTCGTG 62.749 60.000 5.77 0.00 41.75 4.35
2525 4168 3.869272 GGTGCATCGGCTTGCTCG 61.869 66.667 10.10 0.00 43.18 5.03
2527 4170 3.058160 GTGGTGCATCGGCTTGCT 61.058 61.111 10.10 0.00 43.18 3.91
2548 4191 4.909305 CGTGTTGTTGGATGATTGTTGTAC 59.091 41.667 0.00 0.00 0.00 2.90
2552 4195 4.797471 CATCGTGTTGTTGGATGATTGTT 58.203 39.130 0.00 0.00 39.89 2.83
2567 4210 1.600636 CACCACTTGGGCATCGTGT 60.601 57.895 0.00 0.00 42.05 4.49
2603 4246 2.197324 GGTGGCTGGGGTGTTTGA 59.803 61.111 0.00 0.00 0.00 2.69
2624 4267 1.446966 GAGCCAGAAGACTCACGGC 60.447 63.158 0.00 0.00 40.85 5.68
2660 4303 2.680577 CTTGCAGAAGGAAAATGTGCC 58.319 47.619 0.00 0.00 36.32 5.01
2661 4304 2.064014 GCTTGCAGAAGGAAAATGTGC 58.936 47.619 0.00 0.00 37.56 4.57
2681 4324 3.365264 CGGCATATTGATGATTGTTCCGG 60.365 47.826 0.00 0.00 34.73 5.14
2700 4343 5.008019 AGTGTCATTCATTGAATATGTCGGC 59.992 40.000 11.44 1.99 35.70 5.54
2702 4345 8.357796 ACTAGTGTCATTCATTGAATATGTCG 57.642 34.615 11.44 0.08 35.70 4.35
2711 4354 9.264719 TGATATTGCTACTAGTGTCATTCATTG 57.735 33.333 5.39 0.00 0.00 2.82
2726 4369 3.403038 AGTGCCCGAATGATATTGCTAC 58.597 45.455 0.00 0.00 0.00 3.58
2727 4370 3.324846 AGAGTGCCCGAATGATATTGCTA 59.675 43.478 0.00 0.00 0.00 3.49
2728 4371 2.105477 AGAGTGCCCGAATGATATTGCT 59.895 45.455 0.00 0.00 0.00 3.91
2729 4372 2.498167 AGAGTGCCCGAATGATATTGC 58.502 47.619 0.00 0.00 0.00 3.56
2748 4391 4.920927 ACAACAAAACGTGGTTTCAGAAAG 59.079 37.500 0.00 0.00 34.43 2.62
2752 4395 3.570559 ACACAACAAAACGTGGTTTCAG 58.429 40.909 0.00 0.00 34.43 3.02
2758 4404 3.425404 CAGAAGACACAACAAAACGTGG 58.575 45.455 0.00 0.00 37.45 4.94
2762 4408 5.452777 GCTATCCAGAAGACACAACAAAAC 58.547 41.667 0.00 0.00 0.00 2.43
2763 4409 4.518970 GGCTATCCAGAAGACACAACAAAA 59.481 41.667 0.00 0.00 0.00 2.44
2787 4435 6.540189 GCTGTGGGGATAGCTAATGTTATATG 59.460 42.308 0.00 0.00 36.99 1.78
2797 4445 2.158623 CCAATTGCTGTGGGGATAGCTA 60.159 50.000 0.00 0.00 40.52 3.32
2801 4449 3.205815 GCCAATTGCTGTGGGGATA 57.794 52.632 0.00 0.00 36.58 2.59
2802 4450 4.039042 GCCAATTGCTGTGGGGAT 57.961 55.556 0.00 0.00 36.58 3.85
2811 4459 3.006217 AGAAACAGAAGGAAGCCAATTGC 59.994 43.478 0.00 0.00 41.71 3.56
2814 4462 5.505181 TCTAGAAACAGAAGGAAGCCAAT 57.495 39.130 0.00 0.00 0.00 3.16
2816 4464 4.974645 TTCTAGAAACAGAAGGAAGCCA 57.025 40.909 1.68 0.00 31.01 4.75
2817 4465 6.263392 AGTTTTTCTAGAAACAGAAGGAAGCC 59.737 38.462 17.51 0.00 40.98 4.35
2818 4466 7.265647 AGTTTTTCTAGAAACAGAAGGAAGC 57.734 36.000 17.51 3.08 40.98 3.86
2831 4479 8.862325 TGGCAATGATCTAAAGTTTTTCTAGA 57.138 30.769 0.00 0.00 0.00 2.43
2832 4480 9.565213 CTTGGCAATGATCTAAAGTTTTTCTAG 57.435 33.333 0.00 0.00 0.00 2.43
2833 4481 8.028938 GCTTGGCAATGATCTAAAGTTTTTCTA 58.971 33.333 0.00 0.00 0.00 2.10
2834 4482 6.870439 GCTTGGCAATGATCTAAAGTTTTTCT 59.130 34.615 0.00 0.00 0.00 2.52
2836 4484 6.424812 GTGCTTGGCAATGATCTAAAGTTTTT 59.575 34.615 0.00 0.00 41.47 1.94
2854 4502 0.036732 TAGCTTGGGTCAGTGCTTGG 59.963 55.000 0.00 0.00 37.02 3.61
2861 4509 3.091318 CCATGCTAGCTTGGGTCAG 57.909 57.895 32.36 13.63 37.53 3.51
2867 4515 1.066605 GCATCAACCCATGCTAGCTTG 59.933 52.381 20.77 20.77 45.03 4.01
2877 4525 5.355596 CACTTTTAAAGTTGCATCAACCCA 58.644 37.500 7.71 0.00 44.49 4.51
2905 4553 3.407209 AGGTTCATCTGGGGGATTGTAT 58.593 45.455 0.00 0.00 31.27 2.29
2917 4565 4.160626 GGTGTTCAGTAGCTAGGTTCATCT 59.839 45.833 0.00 0.00 0.00 2.90
2938 4586 4.569719 AGTGACCATCTATTTTTCGGGT 57.430 40.909 0.00 0.00 0.00 5.28
2948 4596 5.777223 CCAGGATGAATCTAGTGACCATCTA 59.223 44.000 0.00 0.00 39.69 1.98
2958 4606 9.487790 GAGAAAATAGTTCCAGGATGAATCTAG 57.512 37.037 0.00 0.00 39.69 2.43
2969 4617 4.459337 GTGGGTTGGAGAAAATAGTTCCAG 59.541 45.833 0.00 0.00 41.68 3.86
2972 4620 3.762288 GGGTGGGTTGGAGAAAATAGTTC 59.238 47.826 0.00 0.00 0.00 3.01
2977 4625 1.219213 TGTGGGTGGGTTGGAGAAAAT 59.781 47.619 0.00 0.00 0.00 1.82
2994 4642 9.968870 GAACTAGAGATACCCTACTAAATTGTG 57.031 37.037 0.00 0.00 0.00 3.33
2995 4643 9.710818 TGAACTAGAGATACCCTACTAAATTGT 57.289 33.333 0.00 0.00 0.00 2.71
3014 4662 5.293079 GCTGGTTCTTAAGCATCTGAACTAG 59.707 44.000 15.87 15.87 44.89 2.57
3048 4696 6.505048 TGAGATCTCACCCATGATTATTGT 57.495 37.500 21.67 0.00 34.14 2.71
3059 4707 1.909302 TGGAAGGTTGAGATCTCACCC 59.091 52.381 27.37 27.37 41.85 4.61
3105 4753 9.897744 CTTGTATCAACAACATTATTCACACTT 57.102 29.630 0.00 0.00 40.69 3.16
3188 4839 3.766591 GTGTCAGATTTCTCCCTCTGAGA 59.233 47.826 6.17 0.00 46.29 3.27
3225 4876 7.396339 GGGGTGTTTTCCTAGAAATATGAGTTT 59.604 37.037 0.00 0.00 0.00 2.66
3233 4884 4.463050 TGTGGGGTGTTTTCCTAGAAAT 57.537 40.909 0.00 0.00 0.00 2.17
3234 4885 3.955524 TGTGGGGTGTTTTCCTAGAAA 57.044 42.857 0.00 0.00 0.00 2.52
3245 4896 1.958288 AGAAGAGCTATGTGGGGTGT 58.042 50.000 0.00 0.00 0.00 4.16
3250 4901 7.173218 TGTTTGAGTTTTAGAAGAGCTATGTGG 59.827 37.037 0.00 0.00 0.00 4.17
3259 4910 7.414098 GCTTGTCAGTGTTTGAGTTTTAGAAGA 60.414 37.037 0.00 0.00 36.21 2.87


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

AutoCloner maintained by Alex Coulton.