Multiple sequence alignment - TraesCS4A01G433000

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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 TraesCS4A01G433000 chr4A 100.000 2701 0 0 1862 4562 703651595 703654295 0.000000e+00 4988.0
1 TraesCS4A01G433000 chr4A 97.308 2006 53 1 1863 3868 703605343 703607347 0.000000e+00 3404.0
2 TraesCS4A01G433000 chr4A 97.308 2006 53 1 1863 3868 703707166 703709170 0.000000e+00 3404.0
3 TraesCS4A01G433000 chr4A 100.000 1305 0 0 1 1305 703649734 703651038 0.000000e+00 2410.0
4 TraesCS4A01G433000 chr4A 96.321 1332 22 9 1 1305 703705706 703707037 0.000000e+00 2163.0
5 TraesCS4A01G433000 chr4A 95.823 814 7 8 519 1305 703604427 703605240 0.000000e+00 1290.0
6 TraesCS4A01G433000 chr4A 97.238 543 15 0 1 543 703603862 703604404 0.000000e+00 920.0
7 TraesCS4A01G433000 chr4A 86.535 557 66 3 1950 2506 710284833 710284286 5.050000e-169 604.0
8 TraesCS4A01G433000 chr4A 84.335 549 76 7 1949 2489 710677393 710676847 3.130000e-146 529.0
9 TraesCS4A01G433000 chr4A 92.760 221 12 4 4235 4453 703613034 703613252 2.650000e-82 316.0
10 TraesCS4A01G433000 chr4A 91.071 224 14 5 4235 4455 703714887 703715107 9.590000e-77 298.0
11 TraesCS4A01G433000 chr4A 91.667 192 14 2 3857 4048 662620986 662621175 9.730000e-67 265.0
12 TraesCS4A01G433000 chr4A 95.181 166 7 1 4071 4235 703714592 703714757 1.260000e-65 261.0
13 TraesCS4A01G433000 chr4A 93.578 109 6 1 4071 4178 703612776 703612884 1.310000e-35 161.0
14 TraesCS4A01G433000 chr7A 91.127 1792 113 24 1862 3643 27604543 27606298 0.000000e+00 2386.0
15 TraesCS4A01G433000 chr7A 86.062 1026 130 7 2578 3595 26977667 26976647 0.000000e+00 1090.0
16 TraesCS4A01G433000 chr7A 86.519 994 128 5 2597 3586 26823235 26822244 0.000000e+00 1088.0
17 TraesCS4A01G433000 chr7A 87.687 536 57 3 1971 2506 27032933 27032407 2.330000e-172 616.0
18 TraesCS4A01G433000 chr7A 88.063 511 34 13 811 1305 27603916 27604415 8.510000e-162 580.0
19 TraesCS4A01G433000 chr7A 84.806 566 76 7 1949 2506 26978402 26977839 1.110000e-155 560.0
20 TraesCS4A01G433000 chr7A 92.188 192 13 2 3860 4050 645312703 645312893 2.090000e-68 270.0
21 TraesCS4A01G433000 chr7A 79.297 256 40 11 3617 3868 27606307 27606553 2.820000e-37 167.0
22 TraesCS4A01G433000 chr7A 85.039 127 16 2 4387 4511 709764539 709764414 4.790000e-25 126.0
23 TraesCS4A01G433000 chr7A 91.358 81 6 1 551 630 115736248 115736328 4.830000e-20 110.0
24 TraesCS4A01G433000 chr7A 90.909 55 3 2 4508 4562 695853686 695853634 6.330000e-09 73.1
25 TraesCS4A01G433000 chr7D 91.719 1268 82 13 2498 3752 27243965 27245222 0.000000e+00 1738.0
26 TraesCS4A01G433000 chr7D 86.646 966 129 0 2597 3562 25898025 25897060 0.000000e+00 1070.0
27 TraesCS4A01G433000 chr7D 85.673 1026 134 7 2578 3595 26559498 26558478 0.000000e+00 1068.0
28 TraesCS4A01G433000 chr7D 92.790 638 37 3 1862 2499 27243305 27243933 0.000000e+00 915.0
29 TraesCS4A01G433000 chr7D 83.922 566 81 6 1949 2506 26560223 26559660 2.420000e-147 532.0
30 TraesCS4A01G433000 chr7D 88.674 362 27 9 949 1305 27242827 27243179 3.260000e-116 429.0
31 TraesCS4A01G433000 chr7D 80.000 125 19 5 930 1050 31634771 31634893 2.260000e-13 87.9
32 TraesCS4A01G433000 chr2A 86.293 963 127 3 2601 3562 448294280 448293322 0.000000e+00 1042.0
33 TraesCS4A01G433000 chr2A 87.013 539 59 5 1951 2488 448294893 448294365 8.450000e-167 597.0
34 TraesCS4A01G433000 chr2A 82.301 113 12 6 554 659 568397835 568397946 1.750000e-14 91.6
35 TraesCS4A01G433000 chr2B 82.055 613 95 8 1895 2506 800172551 800171953 4.070000e-140 508.0
36 TraesCS4A01G433000 chr2B 91.327 196 15 2 3856 4049 558109026 558109221 2.710000e-67 267.0
37 TraesCS4A01G433000 chr2B 90.244 82 6 2 553 632 716549836 716549917 6.240000e-19 106.0
38 TraesCS4A01G433000 chr2B 82.727 110 13 6 561 664 43427134 43427243 4.860000e-15 93.5
39 TraesCS4A01G433000 chr2B 92.857 56 3 1 4507 4562 67398648 67398702 3.780000e-11 80.5
40 TraesCS4A01G433000 chr6B 92.228 193 14 1 3860 4052 213152562 213152371 5.820000e-69 272.0
41 TraesCS4A01G433000 chr6B 91.623 191 14 2 3869 4058 471126633 471126444 3.500000e-66 263.0
42 TraesCS4A01G433000 chr6B 94.667 75 3 1 557 630 39369570 39369644 1.040000e-21 115.0
43 TraesCS4A01G433000 chr6B 86.111 108 14 1 4383 4489 75683415 75683522 1.040000e-21 115.0
44 TraesCS4A01G433000 chr3B 92.228 193 12 3 3860 4050 18137979 18138170 2.090000e-68 270.0
45 TraesCS4A01G433000 chr3B 92.105 190 15 0 3859 4048 758070451 758070262 7.520000e-68 268.0
46 TraesCS4A01G433000 chr1D 91.237 194 15 2 3859 4051 299766031 299766223 3.500000e-66 263.0
47 TraesCS4A01G433000 chr1D 77.895 190 23 14 4387 4562 191375257 191375441 2.900000e-17 100.0
48 TraesCS4A01G433000 chr1D 88.235 68 4 2 4494 4559 471132709 471132644 1.360000e-10 78.7
49 TraesCS4A01G433000 chr5B 89.756 205 16 4 3868 4067 643252000 643251796 1.630000e-64 257.0
50 TraesCS4A01G433000 chr6D 85.083 181 22 3 4383 4562 36125426 36125602 3.630000e-41 180.0
51 TraesCS4A01G433000 chr5D 83.708 178 23 4 4387 4562 544897224 544897051 3.650000e-36 163.0
52 TraesCS4A01G433000 chr3A 82.400 125 18 3 4438 4562 442898349 442898229 6.240000e-19 106.0
53 TraesCS4A01G433000 chr4D 87.500 80 9 1 553 631 62231212 62231291 1.750000e-14 91.6
54 TraesCS4A01G433000 chr2D 81.034 116 17 4 555 665 145374602 145374487 2.260000e-13 87.9


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G433000 chr4A 703649734 703654295 4561 False 3699.000000 4988 100.000000 1 4562 2 chr4A.!!$F4 4561
1 TraesCS4A01G433000 chr4A 703705706 703709170 3464 False 2783.500000 3404 96.814500 1 3868 2 chr4A.!!$F5 3867
2 TraesCS4A01G433000 chr4A 703603862 703607347 3485 False 1871.333333 3404 96.789667 1 3868 3 chr4A.!!$F2 3867
3 TraesCS4A01G433000 chr4A 710284286 710284833 547 True 604.000000 604 86.535000 1950 2506 1 chr4A.!!$R1 556
4 TraesCS4A01G433000 chr4A 710676847 710677393 546 True 529.000000 529 84.335000 1949 2489 1 chr4A.!!$R2 540
5 TraesCS4A01G433000 chr4A 703714592 703715107 515 False 279.500000 298 93.126000 4071 4455 2 chr4A.!!$F6 384
6 TraesCS4A01G433000 chr7A 26822244 26823235 991 True 1088.000000 1088 86.519000 2597 3586 1 chr7A.!!$R1 989
7 TraesCS4A01G433000 chr7A 27603916 27606553 2637 False 1044.333333 2386 86.162333 811 3868 3 chr7A.!!$F3 3057
8 TraesCS4A01G433000 chr7A 26976647 26978402 1755 True 825.000000 1090 85.434000 1949 3595 2 chr7A.!!$R5 1646
9 TraesCS4A01G433000 chr7A 27032407 27032933 526 True 616.000000 616 87.687000 1971 2506 1 chr7A.!!$R2 535
10 TraesCS4A01G433000 chr7D 25897060 25898025 965 True 1070.000000 1070 86.646000 2597 3562 1 chr7D.!!$R1 965
11 TraesCS4A01G433000 chr7D 27242827 27245222 2395 False 1027.333333 1738 91.061000 949 3752 3 chr7D.!!$F2 2803
12 TraesCS4A01G433000 chr7D 26558478 26560223 1745 True 800.000000 1068 84.797500 1949 3595 2 chr7D.!!$R2 1646
13 TraesCS4A01G433000 chr2A 448293322 448294893 1571 True 819.500000 1042 86.653000 1951 3562 2 chr2A.!!$R1 1611
14 TraesCS4A01G433000 chr2B 800171953 800172551 598 True 508.000000 508 82.055000 1895 2506 1 chr2B.!!$R1 611

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
913 976 0.747644 CCTCACATACGGGCATGCAA 60.748 55.0 21.36 1.54 0.00 4.08 F
2566 2769 2.103601 ACTCCCGGGTTTATTACATCGG 59.896 50.0 22.86 0.00 41.63 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2881 3127 1.354040 CGAACTGTCAGATGGAGTGC 58.646 55.0 6.91 0.0 0.0 4.40 R
3937 4227 0.248054 GTGTGTGCTGACGTGGTTTG 60.248 55.0 0.00 0.0 0.0 2.93 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
207 208 4.502259 CCACGTCTACCGGTCTAGTAGTAT 60.502 50.000 12.40 0.00 42.24 2.12
218 219 5.035443 GGTCTAGTAGTATTGCAACACTCG 58.965 45.833 14.86 5.70 0.00 4.18
296 297 5.413499 CAGTGTCCCATTTTGATCAAATCC 58.587 41.667 21.10 6.93 32.24 3.01
411 412 2.815647 GGAGCTTGGCGGAAGTCG 60.816 66.667 0.00 0.00 39.79 4.18
502 503 1.057636 ACGCAAACACGTATGACTCG 58.942 50.000 0.00 0.00 46.19 4.18
913 976 0.747644 CCTCACATACGGGCATGCAA 60.748 55.000 21.36 1.54 0.00 4.08
1230 1315 6.056884 AGAACCGACACAATTAGTAACCAAA 58.943 36.000 0.00 0.00 0.00 3.28
2566 2769 2.103601 ACTCCCGGGTTTATTACATCGG 59.896 50.000 22.86 0.00 41.63 4.18
2673 2919 5.097742 TGGACACGATCATAAACTGGATT 57.902 39.130 0.00 0.00 0.00 3.01
2862 3108 3.450904 TGCCATGTCTAAGTTCCTACCT 58.549 45.455 0.00 0.00 0.00 3.08
2881 3127 2.908015 CCATCTACACGGTGGGGG 59.092 66.667 13.48 2.56 0.00 5.40
3288 3536 1.033746 CATTGGAAGGCATCTGCGGT 61.034 55.000 0.00 0.00 43.26 5.68
3615 3904 3.495331 TGATGGGTGTGTAGTGCAATTT 58.505 40.909 0.00 0.00 0.00 1.82
3776 4066 6.597562 GTGGATTACCTGGGATATGTTAACA 58.402 40.000 11.41 11.41 37.04 2.41
3841 4131 5.873712 TGAAAAGAAGCTTCATTTTGTTGCA 59.126 32.000 25.56 17.30 29.34 4.08
3856 4146 5.643379 TTGTTGCAAGATGGAAATACCTC 57.357 39.130 0.00 0.00 39.86 3.85
3870 4160 7.294584 TGGAAATACCTCCATTATTTGTAGGG 58.705 38.462 0.00 0.00 40.71 3.53
3871 4161 7.129660 TGGAAATACCTCCATTATTTGTAGGGA 59.870 37.037 0.00 0.00 40.71 4.20
3872 4162 7.665974 GGAAATACCTCCATTATTTGTAGGGAG 59.334 40.741 0.00 0.00 43.76 4.30
3873 4163 7.707467 AATACCTCCATTATTTGTAGGGAGT 57.293 36.000 0.00 0.00 42.84 3.85
3874 4164 8.808240 AATACCTCCATTATTTGTAGGGAGTA 57.192 34.615 0.00 0.00 42.84 2.59
3875 4165 6.496144 ACCTCCATTATTTGTAGGGAGTAC 57.504 41.667 0.00 0.00 42.84 2.73
3876 4166 5.368816 ACCTCCATTATTTGTAGGGAGTACC 59.631 44.000 0.00 0.00 42.84 3.34
3892 4182 7.842887 GGGAGTACCTAGAACTCATTTAGAT 57.157 40.000 20.28 0.00 44.25 1.98
3893 4183 7.662897 GGGAGTACCTAGAACTCATTTAGATG 58.337 42.308 20.28 0.00 44.25 2.90
3894 4184 7.506261 GGGAGTACCTAGAACTCATTTAGATGA 59.494 40.741 20.28 0.00 44.25 2.92
3929 4219 9.521503 TTGATCACATTCATTTTAAAAACACGA 57.478 25.926 4.44 0.00 0.00 4.35
3930 4220 9.521503 TGATCACATTCATTTTAAAAACACGAA 57.478 25.926 4.44 6.37 0.00 3.85
3931 4221 9.777843 GATCACATTCATTTTAAAAACACGAAC 57.222 29.630 4.44 0.00 0.00 3.95
3932 4222 8.689251 TCACATTCATTTTAAAAACACGAACA 57.311 26.923 4.44 0.00 0.00 3.18
3933 4223 8.802856 TCACATTCATTTTAAAAACACGAACAG 58.197 29.630 4.44 5.51 0.00 3.16
3934 4224 8.802856 CACATTCATTTTAAAAACACGAACAGA 58.197 29.630 4.44 0.00 0.00 3.41
3935 4225 9.528018 ACATTCATTTTAAAAACACGAACAGAT 57.472 25.926 4.44 0.00 0.00 2.90
3942 4232 8.617761 TTTAAAAACACGAACAGATACAAACC 57.382 30.769 0.00 0.00 0.00 3.27
3943 4233 5.821516 AAAACACGAACAGATACAAACCA 57.178 34.783 0.00 0.00 0.00 3.67
3944 4234 4.806342 AACACGAACAGATACAAACCAC 57.194 40.909 0.00 0.00 0.00 4.16
3945 4235 2.798283 ACACGAACAGATACAAACCACG 59.202 45.455 0.00 0.00 0.00 4.94
3946 4236 2.798283 CACGAACAGATACAAACCACGT 59.202 45.455 0.00 0.00 0.00 4.49
3947 4237 3.054878 ACGAACAGATACAAACCACGTC 58.945 45.455 0.00 0.00 0.00 4.34
3948 4238 3.054166 CGAACAGATACAAACCACGTCA 58.946 45.455 0.00 0.00 0.00 4.35
3949 4239 3.121279 CGAACAGATACAAACCACGTCAG 59.879 47.826 0.00 0.00 0.00 3.51
3950 4240 2.413837 ACAGATACAAACCACGTCAGC 58.586 47.619 0.00 0.00 0.00 4.26
3951 4241 2.224185 ACAGATACAAACCACGTCAGCA 60.224 45.455 0.00 0.00 0.00 4.41
3952 4242 2.157668 CAGATACAAACCACGTCAGCAC 59.842 50.000 0.00 0.00 0.00 4.40
3953 4243 2.139917 GATACAAACCACGTCAGCACA 58.860 47.619 0.00 0.00 0.00 4.57
3954 4244 1.292061 TACAAACCACGTCAGCACAC 58.708 50.000 0.00 0.00 0.00 3.82
3955 4245 0.675208 ACAAACCACGTCAGCACACA 60.675 50.000 0.00 0.00 0.00 3.72
3956 4246 0.248054 CAAACCACGTCAGCACACAC 60.248 55.000 0.00 0.00 0.00 3.82
3957 4247 1.701545 AAACCACGTCAGCACACACG 61.702 55.000 0.00 0.00 41.90 4.49
3958 4248 4.000557 CCACGTCAGCACACACGC 62.001 66.667 0.00 0.00 39.73 5.34
3959 4249 2.961721 CACGTCAGCACACACGCT 60.962 61.111 0.00 0.00 45.21 5.07
3960 4250 2.202878 ACGTCAGCACACACGCTT 60.203 55.556 0.00 0.00 41.38 4.68
3961 4251 1.813753 ACGTCAGCACACACGCTTT 60.814 52.632 0.00 0.00 41.38 3.51
3962 4252 1.351707 CGTCAGCACACACGCTTTT 59.648 52.632 0.00 0.00 41.38 2.27
3963 4253 0.248054 CGTCAGCACACACGCTTTTT 60.248 50.000 0.00 0.00 41.38 1.94
3964 4254 1.004398 CGTCAGCACACACGCTTTTTA 60.004 47.619 0.00 0.00 41.38 1.52
3965 4255 2.349438 CGTCAGCACACACGCTTTTTAT 60.349 45.455 0.00 0.00 41.38 1.40
3966 4256 3.120820 CGTCAGCACACACGCTTTTTATA 60.121 43.478 0.00 0.00 41.38 0.98
3967 4257 4.394795 GTCAGCACACACGCTTTTTATAG 58.605 43.478 0.00 0.00 41.38 1.31
3968 4258 3.120338 TCAGCACACACGCTTTTTATAGC 60.120 43.478 0.00 0.00 41.38 2.97
3969 4259 2.811431 AGCACACACGCTTTTTATAGCA 59.189 40.909 0.00 0.00 39.99 3.49
3970 4260 3.440173 AGCACACACGCTTTTTATAGCAT 59.560 39.130 0.00 0.00 39.99 3.79
3971 4261 3.786048 GCACACACGCTTTTTATAGCATC 59.214 43.478 0.00 0.00 41.28 3.91
3972 4262 4.671508 GCACACACGCTTTTTATAGCATCA 60.672 41.667 0.00 0.00 41.28 3.07
3973 4263 4.788100 CACACACGCTTTTTATAGCATCAC 59.212 41.667 0.00 0.00 41.28 3.06
3974 4264 4.454161 ACACACGCTTTTTATAGCATCACA 59.546 37.500 0.00 0.00 41.28 3.58
3975 4265 5.123820 ACACACGCTTTTTATAGCATCACAT 59.876 36.000 0.00 0.00 41.28 3.21
3976 4266 5.678483 CACACGCTTTTTATAGCATCACATC 59.322 40.000 0.00 0.00 41.28 3.06
3977 4267 5.207768 CACGCTTTTTATAGCATCACATCC 58.792 41.667 0.00 0.00 41.28 3.51
3978 4268 4.881273 ACGCTTTTTATAGCATCACATCCA 59.119 37.500 0.00 0.00 41.28 3.41
3979 4269 5.356751 ACGCTTTTTATAGCATCACATCCAA 59.643 36.000 0.00 0.00 41.28 3.53
3980 4270 6.039717 ACGCTTTTTATAGCATCACATCCAAT 59.960 34.615 0.00 0.00 41.28 3.16
3981 4271 6.361481 CGCTTTTTATAGCATCACATCCAATG 59.639 38.462 0.00 0.00 41.28 2.82
3982 4272 6.643770 GCTTTTTATAGCATCACATCCAATGG 59.356 38.462 0.00 0.00 40.89 3.16
3983 4273 5.710513 TTTATAGCATCACATCCAATGGC 57.289 39.130 0.00 0.00 33.60 4.40
3984 4274 3.520691 ATAGCATCACATCCAATGGCT 57.479 42.857 0.00 0.00 33.60 4.75
3985 4275 4.645863 ATAGCATCACATCCAATGGCTA 57.354 40.909 0.00 0.00 33.60 3.93
3986 4276 3.520691 AGCATCACATCCAATGGCTAT 57.479 42.857 0.00 0.00 33.60 2.97
3987 4277 4.645863 AGCATCACATCCAATGGCTATA 57.354 40.909 0.00 0.00 33.60 1.31
3988 4278 4.989277 AGCATCACATCCAATGGCTATAA 58.011 39.130 0.00 0.00 33.60 0.98
3989 4279 5.387788 AGCATCACATCCAATGGCTATAAA 58.612 37.500 0.00 0.00 33.60 1.40
3990 4280 5.834742 AGCATCACATCCAATGGCTATAAAA 59.165 36.000 0.00 0.00 33.60 1.52
3991 4281 6.015688 AGCATCACATCCAATGGCTATAAAAG 60.016 38.462 0.00 0.00 33.60 2.27
3992 4282 6.684686 CATCACATCCAATGGCTATAAAAGG 58.315 40.000 0.00 0.00 33.60 3.11
3993 4283 5.765510 TCACATCCAATGGCTATAAAAGGT 58.234 37.500 0.00 0.00 33.60 3.50
3994 4284 5.593909 TCACATCCAATGGCTATAAAAGGTG 59.406 40.000 0.00 0.00 33.60 4.00
3995 4285 5.593909 CACATCCAATGGCTATAAAAGGTGA 59.406 40.000 0.00 0.00 33.60 4.02
3996 4286 6.096705 CACATCCAATGGCTATAAAAGGTGAA 59.903 38.462 0.00 0.00 33.60 3.18
3997 4287 6.840705 ACATCCAATGGCTATAAAAGGTGAAT 59.159 34.615 0.00 0.00 33.60 2.57
3998 4288 6.713762 TCCAATGGCTATAAAAGGTGAATG 57.286 37.500 0.00 0.00 0.00 2.67
3999 4289 6.430864 TCCAATGGCTATAAAAGGTGAATGA 58.569 36.000 0.00 0.00 0.00 2.57
4000 4290 6.547141 TCCAATGGCTATAAAAGGTGAATGAG 59.453 38.462 0.00 0.00 0.00 2.90
4001 4291 6.547141 CCAATGGCTATAAAAGGTGAATGAGA 59.453 38.462 0.00 0.00 0.00 3.27
4002 4292 7.420800 CAATGGCTATAAAAGGTGAATGAGAC 58.579 38.462 0.00 0.00 0.00 3.36
4003 4293 5.437060 TGGCTATAAAAGGTGAATGAGACC 58.563 41.667 0.00 0.00 0.00 3.85
4004 4294 5.045213 TGGCTATAAAAGGTGAATGAGACCA 60.045 40.000 0.00 0.00 35.76 4.02
4005 4295 5.885912 GGCTATAAAAGGTGAATGAGACCAA 59.114 40.000 0.00 0.00 35.76 3.67
4006 4296 6.377146 GGCTATAAAAGGTGAATGAGACCAAA 59.623 38.462 0.00 0.00 35.76 3.28
4007 4297 7.068716 GGCTATAAAAGGTGAATGAGACCAAAT 59.931 37.037 0.00 0.00 35.76 2.32
4008 4298 8.470002 GCTATAAAAGGTGAATGAGACCAAATT 58.530 33.333 0.00 0.00 35.76 1.82
4014 4304 9.927081 AAAGGTGAATGAGACCAAATTATATCT 57.073 29.630 0.00 0.00 35.76 1.98
4015 4305 9.566432 AAGGTGAATGAGACCAAATTATATCTC 57.434 33.333 0.00 6.03 38.46 2.75
4069 4359 9.997482 ATTTTATAACATTATTCACACCGTGTC 57.003 29.630 0.00 0.00 34.79 3.67
4112 4402 3.590720 CGTCTGCGCATGATTTCATTA 57.409 42.857 12.24 0.00 33.61 1.90
4123 4413 9.611284 GCGCATGATTTCATTAGTTGATTTATA 57.389 29.630 0.30 0.00 33.61 0.98
4162 4453 6.147821 CGCTAGCTTTATGTAGCAATAACCAT 59.852 38.462 13.93 0.00 43.68 3.55
4254 4675 2.436646 CCAACTGCCGCTACAGGG 60.437 66.667 7.63 0.27 42.21 4.45
4289 4710 3.061429 GCGAGTTCATCTTTAGTCTGTGC 59.939 47.826 0.00 0.00 0.00 4.57
4294 4715 3.325870 TCATCTTTAGTCTGTGCAACCG 58.674 45.455 0.00 0.00 34.36 4.44
4298 4719 2.741486 TTAGTCTGTGCAACCGGCCC 62.741 60.000 0.00 0.00 43.89 5.80
4316 4737 2.322081 CCGCGTGTTAACCACCTGG 61.322 63.158 4.92 0.00 41.26 4.45
4346 4767 0.963962 CAAGAGCACAACCAGCCATT 59.036 50.000 0.00 0.00 0.00 3.16
4348 4769 0.610232 AGAGCACAACCAGCCATTCC 60.610 55.000 0.00 0.00 0.00 3.01
4349 4770 0.895100 GAGCACAACCAGCCATTCCA 60.895 55.000 0.00 0.00 0.00 3.53
4350 4771 0.896940 AGCACAACCAGCCATTCCAG 60.897 55.000 0.00 0.00 0.00 3.86
4351 4772 1.588082 CACAACCAGCCATTCCAGC 59.412 57.895 0.00 0.00 0.00 4.85
4352 4773 0.896940 CACAACCAGCCATTCCAGCT 60.897 55.000 0.00 0.00 42.70 4.24
4357 4778 2.362120 AGCCATTCCAGCTGCCAC 60.362 61.111 8.66 0.00 39.69 5.01
4358 4779 2.677524 GCCATTCCAGCTGCCACA 60.678 61.111 8.66 0.00 0.00 4.17
4386 4809 1.852067 CTCCGCCCCTTTTTGTGTCG 61.852 60.000 0.00 0.00 0.00 4.35
4403 4826 6.301687 TGTGTCGAGTAATGCTAGAGATAC 57.698 41.667 0.00 0.00 29.47 2.24
4416 4839 7.422878 TGCTAGAGATACATAGAGTTACACG 57.577 40.000 0.00 0.00 0.00 4.49
4427 4850 7.495055 ACATAGAGTTACACGGGGTTTATAAG 58.505 38.462 0.00 0.00 0.00 1.73
4432 4855 1.631898 ACACGGGGTTTATAAGCTGGT 59.368 47.619 0.00 0.00 0.00 4.00
4433 4856 2.014128 CACGGGGTTTATAAGCTGGTG 58.986 52.381 0.00 2.40 0.00 4.17
4435 4858 2.285977 CGGGGTTTATAAGCTGGTGAC 58.714 52.381 0.00 0.00 0.00 3.67
4441 4864 5.007682 GGTTTATAAGCTGGTGACCTTTGA 58.992 41.667 2.11 0.00 0.00 2.69
4455 4878 6.180472 GTGACCTTTGATTGGAGATTAAGGA 58.820 40.000 0.00 0.00 36.50 3.36
4456 4879 6.830838 GTGACCTTTGATTGGAGATTAAGGAT 59.169 38.462 0.00 0.00 36.50 3.24
4457 4880 6.830324 TGACCTTTGATTGGAGATTAAGGATG 59.170 38.462 0.00 0.00 36.50 3.51
4458 4881 6.973642 ACCTTTGATTGGAGATTAAGGATGA 58.026 36.000 0.00 0.00 36.50 2.92
4459 4882 7.059156 ACCTTTGATTGGAGATTAAGGATGAG 58.941 38.462 0.00 0.00 36.50 2.90
4460 4883 6.489361 CCTTTGATTGGAGATTAAGGATGAGG 59.511 42.308 0.00 0.00 35.30 3.86
4461 4884 6.829985 TTGATTGGAGATTAAGGATGAGGA 57.170 37.500 0.00 0.00 0.00 3.71
4462 4885 6.430962 TGATTGGAGATTAAGGATGAGGAG 57.569 41.667 0.00 0.00 0.00 3.69
4463 4886 5.309020 TGATTGGAGATTAAGGATGAGGAGG 59.691 44.000 0.00 0.00 0.00 4.30
4464 4887 3.591789 TGGAGATTAAGGATGAGGAGGG 58.408 50.000 0.00 0.00 0.00 4.30
4465 4888 2.909662 GGAGATTAAGGATGAGGAGGGG 59.090 54.545 0.00 0.00 0.00 4.79
4466 4889 2.304470 GAGATTAAGGATGAGGAGGGGC 59.696 54.545 0.00 0.00 0.00 5.80
4467 4890 1.352687 GATTAAGGATGAGGAGGGGCC 59.647 57.143 0.00 0.00 0.00 5.80
4468 4891 1.054406 TTAAGGATGAGGAGGGGCCG 61.054 60.000 0.00 0.00 43.43 6.13
4469 4892 1.956639 TAAGGATGAGGAGGGGCCGA 61.957 60.000 0.00 0.00 43.43 5.54
4470 4893 3.551407 GGATGAGGAGGGGCCGAC 61.551 72.222 0.00 0.00 43.43 4.79
4471 4894 3.551407 GATGAGGAGGGGCCGACC 61.551 72.222 9.20 9.20 43.43 4.79
4481 4904 4.646877 GGCCGACCCCCGTGAAAA 62.647 66.667 0.00 0.00 36.31 2.29
4482 4905 2.360726 GCCGACCCCCGTGAAAAT 60.361 61.111 0.00 0.00 36.31 1.82
4483 4906 2.404186 GCCGACCCCCGTGAAAATC 61.404 63.158 0.00 0.00 36.31 2.17
4484 4907 1.003112 CCGACCCCCGTGAAAATCA 60.003 57.895 0.00 0.00 36.31 2.57
4485 4908 1.024579 CCGACCCCCGTGAAAATCAG 61.025 60.000 0.00 0.00 36.31 2.90
4486 4909 1.024579 CGACCCCCGTGAAAATCAGG 61.025 60.000 0.00 0.00 32.49 3.86
4492 4915 2.418368 CCGTGAAAATCAGGGGATGA 57.582 50.000 10.48 0.00 45.83 2.92
4493 4916 2.292267 CCGTGAAAATCAGGGGATGAG 58.708 52.381 10.48 0.00 45.83 2.90
4494 4917 2.292267 CGTGAAAATCAGGGGATGAGG 58.708 52.381 0.00 0.00 42.53 3.86
4495 4918 2.356125 CGTGAAAATCAGGGGATGAGGT 60.356 50.000 0.00 0.00 42.53 3.85
4496 4919 3.701664 GTGAAAATCAGGGGATGAGGTT 58.298 45.455 0.00 0.00 42.53 3.50
4497 4920 4.625324 CGTGAAAATCAGGGGATGAGGTTA 60.625 45.833 0.00 0.00 42.53 2.85
4498 4921 4.884164 GTGAAAATCAGGGGATGAGGTTAG 59.116 45.833 0.00 0.00 42.53 2.34
4499 4922 4.540099 TGAAAATCAGGGGATGAGGTTAGT 59.460 41.667 0.00 0.00 42.53 2.24
4500 4923 5.015178 TGAAAATCAGGGGATGAGGTTAGTT 59.985 40.000 0.00 0.00 42.53 2.24
4501 4924 6.216662 TGAAAATCAGGGGATGAGGTTAGTTA 59.783 38.462 0.00 0.00 42.53 2.24
4502 4925 5.896073 AATCAGGGGATGAGGTTAGTTAG 57.104 43.478 0.00 0.00 42.53 2.34
4503 4926 4.620086 TCAGGGGATGAGGTTAGTTAGA 57.380 45.455 0.00 0.00 32.77 2.10
4504 4927 4.955335 TCAGGGGATGAGGTTAGTTAGAA 58.045 43.478 0.00 0.00 32.77 2.10
4505 4928 5.347124 TCAGGGGATGAGGTTAGTTAGAAA 58.653 41.667 0.00 0.00 32.77 2.52
4506 4929 5.425539 TCAGGGGATGAGGTTAGTTAGAAAG 59.574 44.000 0.00 0.00 32.77 2.62
4507 4930 5.425539 CAGGGGATGAGGTTAGTTAGAAAGA 59.574 44.000 0.00 0.00 0.00 2.52
4508 4931 6.030082 AGGGGATGAGGTTAGTTAGAAAGAA 58.970 40.000 0.00 0.00 0.00 2.52
4509 4932 6.504279 AGGGGATGAGGTTAGTTAGAAAGAAA 59.496 38.462 0.00 0.00 0.00 2.52
4510 4933 6.824196 GGGGATGAGGTTAGTTAGAAAGAAAG 59.176 42.308 0.00 0.00 0.00 2.62
4511 4934 7.311109 GGGGATGAGGTTAGTTAGAAAGAAAGA 60.311 40.741 0.00 0.00 0.00 2.52
4512 4935 8.101419 GGGATGAGGTTAGTTAGAAAGAAAGAA 58.899 37.037 0.00 0.00 0.00 2.52
4513 4936 9.503399 GGATGAGGTTAGTTAGAAAGAAAGAAA 57.497 33.333 0.00 0.00 0.00 2.52
4526 4949 8.614469 AGAAAGAAAGAAAATCCTAGTCAGTG 57.386 34.615 0.00 0.00 0.00 3.66
4527 4950 8.214364 AGAAAGAAAGAAAATCCTAGTCAGTGT 58.786 33.333 0.00 0.00 0.00 3.55
4528 4951 7.736447 AAGAAAGAAAATCCTAGTCAGTGTG 57.264 36.000 0.00 0.00 0.00 3.82
4529 4952 6.831976 AGAAAGAAAATCCTAGTCAGTGTGT 58.168 36.000 0.00 0.00 0.00 3.72
4530 4953 7.963532 AGAAAGAAAATCCTAGTCAGTGTGTA 58.036 34.615 0.00 0.00 0.00 2.90
4531 4954 8.429641 AGAAAGAAAATCCTAGTCAGTGTGTAA 58.570 33.333 0.00 0.00 0.00 2.41
4532 4955 9.220767 GAAAGAAAATCCTAGTCAGTGTGTAAT 57.779 33.333 0.00 0.00 0.00 1.89
4533 4956 9.574516 AAAGAAAATCCTAGTCAGTGTGTAATT 57.425 29.630 0.00 0.00 0.00 1.40
4534 4957 8.553459 AGAAAATCCTAGTCAGTGTGTAATTG 57.447 34.615 0.00 0.00 0.00 2.32
4535 4958 6.743575 AAATCCTAGTCAGTGTGTAATTGC 57.256 37.500 0.00 0.00 0.00 3.56
4536 4959 3.845178 TCCTAGTCAGTGTGTAATTGCG 58.155 45.455 0.00 0.00 0.00 4.85
4537 4960 3.257375 TCCTAGTCAGTGTGTAATTGCGT 59.743 43.478 0.00 0.00 0.00 5.24
4538 4961 3.367932 CCTAGTCAGTGTGTAATTGCGTG 59.632 47.826 0.00 0.00 0.00 5.34
4539 4962 2.833794 AGTCAGTGTGTAATTGCGTGT 58.166 42.857 0.00 0.00 0.00 4.49
4540 4963 3.985008 AGTCAGTGTGTAATTGCGTGTA 58.015 40.909 0.00 0.00 0.00 2.90
4541 4964 4.373527 AGTCAGTGTGTAATTGCGTGTAA 58.626 39.130 0.00 0.00 0.00 2.41
4542 4965 4.210537 AGTCAGTGTGTAATTGCGTGTAAC 59.789 41.667 0.00 0.00 0.00 2.50
4543 4966 4.210537 GTCAGTGTGTAATTGCGTGTAACT 59.789 41.667 0.00 0.00 31.75 2.24
4544 4967 4.446385 TCAGTGTGTAATTGCGTGTAACTC 59.554 41.667 0.00 0.00 31.75 3.01
4545 4968 4.447724 CAGTGTGTAATTGCGTGTAACTCT 59.552 41.667 0.00 0.00 31.75 3.24
4546 4969 5.050363 CAGTGTGTAATTGCGTGTAACTCTT 60.050 40.000 0.00 0.00 31.75 2.85
4547 4970 5.526111 AGTGTGTAATTGCGTGTAACTCTTT 59.474 36.000 0.00 0.00 31.75 2.52
4548 4971 6.702723 AGTGTGTAATTGCGTGTAACTCTTTA 59.297 34.615 0.00 0.00 31.75 1.85
4549 4972 7.386848 AGTGTGTAATTGCGTGTAACTCTTTAT 59.613 33.333 0.00 0.00 31.75 1.40
4550 4973 8.649841 GTGTGTAATTGCGTGTAACTCTTTATA 58.350 33.333 0.00 0.00 31.75 0.98
4551 4974 8.649841 TGTGTAATTGCGTGTAACTCTTTATAC 58.350 33.333 0.00 0.00 31.75 1.47
4559 4982 7.496704 CGTGTAACTCTTTATACGTTTAGCA 57.503 36.000 0.00 0.00 43.81 3.49
4560 4983 8.112099 CGTGTAACTCTTTATACGTTTAGCAT 57.888 34.615 0.00 0.00 43.81 3.79
4561 4984 8.589629 CGTGTAACTCTTTATACGTTTAGCATT 58.410 33.333 0.00 0.00 43.81 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.337396 TGTTAAATGTATCATCATAGTGTTCCC 57.663 33.333 0.00 0.00 0.00 3.97
136 137 4.932799 CGTCACTAGATAGATGGATCGTCT 59.067 45.833 0.00 4.85 33.90 4.18
207 208 0.736053 GGTTTCACCGAGTGTTGCAA 59.264 50.000 0.00 0.00 34.79 4.08
218 219 4.610945 CATTCTTCTGTGTTGGTTTCACC 58.389 43.478 0.00 0.00 39.22 4.02
296 297 2.279517 GCACCGCCTCTCCGTATG 60.280 66.667 0.00 0.00 0.00 2.39
411 412 4.585955 TCTCATCCACCGAGCTATTAAC 57.414 45.455 0.00 0.00 0.00 2.01
680 740 6.159988 CCCATAAAAGAAAATAAACACGGCA 58.840 36.000 0.00 0.00 0.00 5.69
720 780 6.909550 AAACCCATAAAAGAAGCATGTGTA 57.090 33.333 0.00 0.00 0.00 2.90
2673 2919 2.682136 TCCTTGGGCATCGACGGA 60.682 61.111 0.00 0.00 0.00 4.69
2881 3127 1.354040 CGAACTGTCAGATGGAGTGC 58.646 55.000 6.91 0.00 0.00 4.40
3288 3536 2.560119 GCAAACCATCGGCACACCA 61.560 57.895 0.00 0.00 34.57 4.17
3615 3904 6.620877 AATGACAACCCTGACTTCTACATA 57.379 37.500 0.00 0.00 0.00 2.29
3674 3963 9.892130 ACATCTTAATAAACTCTTCGGATTCTT 57.108 29.630 0.00 0.00 0.00 2.52
3776 4066 2.332063 ATTTCCATCGTCTTCGGCAT 57.668 45.000 0.00 0.00 37.69 4.40
3856 4146 7.850935 TCTAGGTACTCCCTACAAATAATGG 57.149 40.000 0.00 0.00 43.87 3.16
3868 4158 7.506261 TCATCTAAATGAGTTCTAGGTACTCCC 59.494 40.741 17.72 2.30 41.02 4.30
3869 4159 8.466617 TCATCTAAATGAGTTCTAGGTACTCC 57.533 38.462 17.72 6.18 41.02 3.85
3903 4193 9.521503 TCGTGTTTTTAAAATGAATGTGATCAA 57.478 25.926 0.00 0.00 32.06 2.57
3904 4194 9.521503 TTCGTGTTTTTAAAATGAATGTGATCA 57.478 25.926 0.55 0.00 0.00 2.92
3905 4195 9.777843 GTTCGTGTTTTTAAAATGAATGTGATC 57.222 29.630 0.55 0.00 0.00 2.92
3906 4196 9.307121 TGTTCGTGTTTTTAAAATGAATGTGAT 57.693 25.926 0.55 0.00 0.00 3.06
3907 4197 8.689251 TGTTCGTGTTTTTAAAATGAATGTGA 57.311 26.923 0.55 0.00 0.00 3.58
3908 4198 8.802856 TCTGTTCGTGTTTTTAAAATGAATGTG 58.197 29.630 0.55 1.06 0.00 3.21
3909 4199 8.918961 TCTGTTCGTGTTTTTAAAATGAATGT 57.081 26.923 0.55 0.00 0.00 2.71
3916 4206 9.074443 GGTTTGTATCTGTTCGTGTTTTTAAAA 57.926 29.630 0.00 0.00 0.00 1.52
3917 4207 8.242053 TGGTTTGTATCTGTTCGTGTTTTTAAA 58.758 29.630 0.00 0.00 0.00 1.52
3918 4208 7.697291 GTGGTTTGTATCTGTTCGTGTTTTTAA 59.303 33.333 0.00 0.00 0.00 1.52
3919 4209 7.188157 GTGGTTTGTATCTGTTCGTGTTTTTA 58.812 34.615 0.00 0.00 0.00 1.52
3920 4210 6.031471 GTGGTTTGTATCTGTTCGTGTTTTT 58.969 36.000 0.00 0.00 0.00 1.94
3921 4211 5.575019 GTGGTTTGTATCTGTTCGTGTTTT 58.425 37.500 0.00 0.00 0.00 2.43
3922 4212 4.260456 CGTGGTTTGTATCTGTTCGTGTTT 60.260 41.667 0.00 0.00 0.00 2.83
3923 4213 3.246699 CGTGGTTTGTATCTGTTCGTGTT 59.753 43.478 0.00 0.00 0.00 3.32
3924 4214 2.798283 CGTGGTTTGTATCTGTTCGTGT 59.202 45.455 0.00 0.00 0.00 4.49
3925 4215 2.798283 ACGTGGTTTGTATCTGTTCGTG 59.202 45.455 0.00 0.00 0.00 4.35
3926 4216 3.054878 GACGTGGTTTGTATCTGTTCGT 58.945 45.455 0.00 0.00 0.00 3.85
3927 4217 3.054166 TGACGTGGTTTGTATCTGTTCG 58.946 45.455 0.00 0.00 0.00 3.95
3928 4218 3.120649 GCTGACGTGGTTTGTATCTGTTC 60.121 47.826 0.00 0.00 0.00 3.18
3929 4219 2.806244 GCTGACGTGGTTTGTATCTGTT 59.194 45.455 0.00 0.00 0.00 3.16
3930 4220 2.224185 TGCTGACGTGGTTTGTATCTGT 60.224 45.455 0.00 0.00 0.00 3.41
3931 4221 2.157668 GTGCTGACGTGGTTTGTATCTG 59.842 50.000 0.00 0.00 0.00 2.90
3932 4222 2.224185 TGTGCTGACGTGGTTTGTATCT 60.224 45.455 0.00 0.00 0.00 1.98
3933 4223 2.096417 GTGTGCTGACGTGGTTTGTATC 60.096 50.000 0.00 0.00 0.00 2.24
3934 4224 1.871039 GTGTGCTGACGTGGTTTGTAT 59.129 47.619 0.00 0.00 0.00 2.29
3935 4225 1.292061 GTGTGCTGACGTGGTTTGTA 58.708 50.000 0.00 0.00 0.00 2.41
3936 4226 0.675208 TGTGTGCTGACGTGGTTTGT 60.675 50.000 0.00 0.00 0.00 2.83
3937 4227 0.248054 GTGTGTGCTGACGTGGTTTG 60.248 55.000 0.00 0.00 0.00 2.93
3938 4228 1.701545 CGTGTGTGCTGACGTGGTTT 61.702 55.000 0.00 0.00 0.00 3.27
3939 4229 2.171079 CGTGTGTGCTGACGTGGTT 61.171 57.895 0.00 0.00 0.00 3.67
3940 4230 2.584970 CGTGTGTGCTGACGTGGT 60.585 61.111 0.00 0.00 0.00 4.16
3941 4231 4.000557 GCGTGTGTGCTGACGTGG 62.001 66.667 0.00 0.00 37.89 4.94
3942 4232 2.035617 AAAGCGTGTGTGCTGACGTG 62.036 55.000 0.00 0.00 46.60 4.49
3943 4233 1.366111 AAAAGCGTGTGTGCTGACGT 61.366 50.000 0.00 0.00 46.60 4.34
3944 4234 0.248054 AAAAAGCGTGTGTGCTGACG 60.248 50.000 0.00 0.00 46.60 4.35
3945 4235 2.748461 TAAAAAGCGTGTGTGCTGAC 57.252 45.000 0.00 0.00 46.60 3.51
3946 4236 3.120338 GCTATAAAAAGCGTGTGTGCTGA 60.120 43.478 0.00 0.00 46.60 4.26
3947 4237 3.163594 GCTATAAAAAGCGTGTGTGCTG 58.836 45.455 0.00 0.00 46.60 4.41
3949 4239 3.196007 TGCTATAAAAAGCGTGTGTGC 57.804 42.857 0.00 0.00 45.85 4.57
3950 4240 4.788100 GTGATGCTATAAAAAGCGTGTGTG 59.212 41.667 0.00 0.00 45.85 3.82
3951 4241 4.454161 TGTGATGCTATAAAAAGCGTGTGT 59.546 37.500 0.00 0.00 45.85 3.72
3952 4242 4.968626 TGTGATGCTATAAAAAGCGTGTG 58.031 39.130 0.00 0.00 45.85 3.82
3953 4243 5.220854 GGATGTGATGCTATAAAAAGCGTGT 60.221 40.000 0.00 0.00 45.85 4.49
3954 4244 5.207768 GGATGTGATGCTATAAAAAGCGTG 58.792 41.667 0.00 0.00 45.85 5.34
3955 4245 4.881273 TGGATGTGATGCTATAAAAAGCGT 59.119 37.500 0.00 0.00 45.85 5.07
3956 4246 5.422666 TGGATGTGATGCTATAAAAAGCG 57.577 39.130 0.00 0.00 45.85 4.68
3957 4247 6.643770 CCATTGGATGTGATGCTATAAAAAGC 59.356 38.462 0.00 0.00 43.08 3.51
3958 4248 6.643770 GCCATTGGATGTGATGCTATAAAAAG 59.356 38.462 6.95 0.00 0.00 2.27
3959 4249 6.324512 AGCCATTGGATGTGATGCTATAAAAA 59.675 34.615 6.95 0.00 0.00 1.94
3960 4250 5.834742 AGCCATTGGATGTGATGCTATAAAA 59.165 36.000 6.95 0.00 0.00 1.52
3961 4251 5.387788 AGCCATTGGATGTGATGCTATAAA 58.612 37.500 6.95 0.00 0.00 1.40
3962 4252 4.989277 AGCCATTGGATGTGATGCTATAA 58.011 39.130 6.95 0.00 0.00 0.98
3963 4253 4.645863 AGCCATTGGATGTGATGCTATA 57.354 40.909 6.95 0.00 0.00 1.31
3964 4254 3.520691 AGCCATTGGATGTGATGCTAT 57.479 42.857 6.95 0.00 0.00 2.97
3965 4255 4.645863 ATAGCCATTGGATGTGATGCTA 57.354 40.909 6.95 0.00 0.00 3.49
3966 4256 3.520691 ATAGCCATTGGATGTGATGCT 57.479 42.857 6.95 0.00 0.00 3.79
3967 4257 5.710513 TTTATAGCCATTGGATGTGATGC 57.289 39.130 6.95 0.00 0.00 3.91
3968 4258 6.266103 ACCTTTTATAGCCATTGGATGTGATG 59.734 38.462 6.95 0.00 0.00 3.07
3969 4259 6.266103 CACCTTTTATAGCCATTGGATGTGAT 59.734 38.462 6.95 0.00 0.00 3.06
3970 4260 5.593909 CACCTTTTATAGCCATTGGATGTGA 59.406 40.000 6.95 0.00 0.00 3.58
3971 4261 5.593909 TCACCTTTTATAGCCATTGGATGTG 59.406 40.000 6.95 2.95 0.00 3.21
3972 4262 5.765510 TCACCTTTTATAGCCATTGGATGT 58.234 37.500 6.95 0.10 0.00 3.06
3973 4263 6.713762 TTCACCTTTTATAGCCATTGGATG 57.286 37.500 6.95 0.00 0.00 3.51
3974 4264 7.068702 TCATTCACCTTTTATAGCCATTGGAT 58.931 34.615 6.95 1.78 0.00 3.41
3975 4265 6.430864 TCATTCACCTTTTATAGCCATTGGA 58.569 36.000 6.95 0.00 0.00 3.53
3976 4266 6.547141 TCTCATTCACCTTTTATAGCCATTGG 59.453 38.462 0.00 0.00 0.00 3.16
3977 4267 7.420800 GTCTCATTCACCTTTTATAGCCATTG 58.579 38.462 0.00 0.00 0.00 2.82
3978 4268 6.547510 GGTCTCATTCACCTTTTATAGCCATT 59.452 38.462 0.00 0.00 0.00 3.16
3979 4269 6.064717 GGTCTCATTCACCTTTTATAGCCAT 58.935 40.000 0.00 0.00 0.00 4.40
3980 4270 5.045213 TGGTCTCATTCACCTTTTATAGCCA 60.045 40.000 0.00 0.00 34.66 4.75
3981 4271 5.437060 TGGTCTCATTCACCTTTTATAGCC 58.563 41.667 0.00 0.00 34.66 3.93
3982 4272 7.391148 TTTGGTCTCATTCACCTTTTATAGC 57.609 36.000 0.00 0.00 34.66 2.97
3988 4278 9.927081 AGATATAATTTGGTCTCATTCACCTTT 57.073 29.630 0.00 0.00 34.66 3.11
3989 4279 9.566432 GAGATATAATTTGGTCTCATTCACCTT 57.434 33.333 8.11 0.00 37.60 3.50
3990 4280 8.717717 TGAGATATAATTTGGTCTCATTCACCT 58.282 33.333 10.50 0.00 41.40 4.00
3991 4281 8.908786 TGAGATATAATTTGGTCTCATTCACC 57.091 34.615 10.50 0.00 41.40 4.02
4043 4333 9.997482 GACACGGTGTGAATAATGTTATAAAAT 57.003 29.630 20.06 0.00 36.96 1.82
4044 4334 8.452534 GGACACGGTGTGAATAATGTTATAAAA 58.547 33.333 20.06 0.00 36.96 1.52
4045 4335 7.606839 TGGACACGGTGTGAATAATGTTATAAA 59.393 33.333 20.06 0.00 36.96 1.40
4046 4336 7.104290 TGGACACGGTGTGAATAATGTTATAA 58.896 34.615 20.06 0.00 36.96 0.98
4047 4337 6.641474 TGGACACGGTGTGAATAATGTTATA 58.359 36.000 20.06 0.00 36.96 0.98
4048 4338 5.492895 TGGACACGGTGTGAATAATGTTAT 58.507 37.500 20.06 0.00 36.96 1.89
4049 4339 4.895961 TGGACACGGTGTGAATAATGTTA 58.104 39.130 20.06 0.00 36.96 2.41
4050 4340 3.745799 TGGACACGGTGTGAATAATGTT 58.254 40.909 20.06 0.00 36.96 2.71
4051 4341 3.410631 TGGACACGGTGTGAATAATGT 57.589 42.857 20.06 0.00 36.96 2.71
4052 4342 3.500299 TGTTGGACACGGTGTGAATAATG 59.500 43.478 20.06 0.00 36.96 1.90
4053 4343 3.745799 TGTTGGACACGGTGTGAATAAT 58.254 40.909 20.06 0.00 36.96 1.28
4054 4344 3.195471 TGTTGGACACGGTGTGAATAA 57.805 42.857 20.06 5.36 36.96 1.40
4055 4345 2.912690 TGTTGGACACGGTGTGAATA 57.087 45.000 20.06 6.73 36.96 1.75
4056 4346 2.270352 ATGTTGGACACGGTGTGAAT 57.730 45.000 20.06 2.02 36.96 2.57
4057 4347 1.673400 CAATGTTGGACACGGTGTGAA 59.327 47.619 20.06 8.31 36.96 3.18
4058 4348 1.134371 TCAATGTTGGACACGGTGTGA 60.134 47.619 20.06 4.08 36.96 3.58
4059 4349 1.304254 TCAATGTTGGACACGGTGTG 58.696 50.000 20.06 0.78 39.75 3.82
4060 4350 2.270352 ATCAATGTTGGACACGGTGT 57.730 45.000 14.66 14.66 0.00 4.16
4061 4351 2.095263 GGAATCAATGTTGGACACGGTG 60.095 50.000 6.58 6.58 0.00 4.94
4062 4352 2.159382 GGAATCAATGTTGGACACGGT 58.841 47.619 0.00 0.00 0.00 4.83
4063 4353 2.158559 TGGAATCAATGTTGGACACGG 58.841 47.619 0.00 0.00 0.00 4.94
4064 4354 3.073678 TCTGGAATCAATGTTGGACACG 58.926 45.455 0.00 0.00 0.00 4.49
4065 4355 5.649782 ATTCTGGAATCAATGTTGGACAC 57.350 39.130 0.00 0.00 0.00 3.67
4066 4356 6.457355 CAAATTCTGGAATCAATGTTGGACA 58.543 36.000 0.00 0.00 0.00 4.02
4067 4357 6.956299 CAAATTCTGGAATCAATGTTGGAC 57.044 37.500 0.00 0.00 0.00 4.02
4092 4382 2.463553 AATGAAATCATGCGCAGACG 57.536 45.000 18.32 7.12 37.78 4.18
4093 4383 4.542662 ACTAATGAAATCATGCGCAGAC 57.457 40.909 18.32 3.85 36.56 3.51
4095 4385 4.912214 TCAACTAATGAAATCATGCGCAG 58.088 39.130 18.32 8.46 36.56 5.18
4112 4402 8.495949 CGCTATCAAAACCGATATAAATCAACT 58.504 33.333 0.00 0.00 31.93 3.16
4123 4413 2.135933 GCTAGCGCTATCAAAACCGAT 58.864 47.619 19.19 0.00 0.00 4.18
4316 4737 0.375106 GTGCTCTTGCGGTCTATTGC 59.625 55.000 0.00 0.00 43.34 3.56
4354 4775 2.475466 GCGGAGATGTGCCATGTGG 61.475 63.158 0.00 0.00 38.53 4.17
4373 4796 3.502211 AGCATTACTCGACACAAAAAGGG 59.498 43.478 0.00 0.00 0.00 3.95
4403 4826 6.423001 GCTTATAAACCCCGTGTAACTCTATG 59.577 42.308 0.00 0.00 31.75 2.23
4414 4837 1.910671 TCACCAGCTTATAAACCCCGT 59.089 47.619 0.00 0.00 0.00 5.28
4416 4839 2.241430 AGGTCACCAGCTTATAAACCCC 59.759 50.000 0.00 0.00 0.00 4.95
4427 4850 1.815003 CTCCAATCAAAGGTCACCAGC 59.185 52.381 0.00 0.00 0.00 4.85
4432 4855 6.387192 TCCTTAATCTCCAATCAAAGGTCA 57.613 37.500 0.00 0.00 35.91 4.02
4433 4856 7.056635 TCATCCTTAATCTCCAATCAAAGGTC 58.943 38.462 0.00 0.00 35.91 3.85
4435 4858 6.489361 CCTCATCCTTAATCTCCAATCAAAGG 59.511 42.308 0.00 0.00 35.80 3.11
4441 4864 4.600983 CCCTCCTCATCCTTAATCTCCAAT 59.399 45.833 0.00 0.00 0.00 3.16
4464 4887 3.931190 ATTTTCACGGGGGTCGGCC 62.931 63.158 0.00 0.00 44.45 6.13
4465 4888 2.360726 ATTTTCACGGGGGTCGGC 60.361 61.111 0.00 0.00 44.45 5.54
4466 4889 1.003112 TGATTTTCACGGGGGTCGG 60.003 57.895 0.00 0.00 44.45 4.79
4467 4890 1.024579 CCTGATTTTCACGGGGGTCG 61.025 60.000 0.00 0.00 45.88 4.79
4468 4891 0.679960 CCCTGATTTTCACGGGGGTC 60.680 60.000 0.00 0.00 46.89 4.46
4469 4892 1.382629 CCCTGATTTTCACGGGGGT 59.617 57.895 0.00 0.00 46.89 4.95
4470 4893 4.337013 CCCTGATTTTCACGGGGG 57.663 61.111 0.00 0.00 46.89 5.40
4472 4895 1.064758 TCATCCCCTGATTTTCACGGG 60.065 52.381 5.49 5.49 42.06 5.28
4473 4896 2.292267 CTCATCCCCTGATTTTCACGG 58.708 52.381 0.00 0.00 32.10 4.94
4474 4897 2.292267 CCTCATCCCCTGATTTTCACG 58.708 52.381 0.00 0.00 32.10 4.35
4475 4898 3.372440 ACCTCATCCCCTGATTTTCAC 57.628 47.619 0.00 0.00 32.10 3.18
4476 4899 4.540099 ACTAACCTCATCCCCTGATTTTCA 59.460 41.667 0.00 0.00 32.10 2.69
4477 4900 5.117406 ACTAACCTCATCCCCTGATTTTC 57.883 43.478 0.00 0.00 32.10 2.29
4478 4901 5.536497 AACTAACCTCATCCCCTGATTTT 57.464 39.130 0.00 0.00 32.10 1.82
4479 4902 5.970640 TCTAACTAACCTCATCCCCTGATTT 59.029 40.000 0.00 0.00 32.10 2.17
4480 4903 5.538877 TCTAACTAACCTCATCCCCTGATT 58.461 41.667 0.00 0.00 32.10 2.57
4481 4904 5.157770 TCTAACTAACCTCATCCCCTGAT 57.842 43.478 0.00 0.00 32.10 2.90
4482 4905 4.620086 TCTAACTAACCTCATCCCCTGA 57.380 45.455 0.00 0.00 0.00 3.86
4483 4906 5.425539 TCTTTCTAACTAACCTCATCCCCTG 59.574 44.000 0.00 0.00 0.00 4.45
4484 4907 5.600749 TCTTTCTAACTAACCTCATCCCCT 58.399 41.667 0.00 0.00 0.00 4.79
4485 4908 5.952347 TCTTTCTAACTAACCTCATCCCC 57.048 43.478 0.00 0.00 0.00 4.81
4486 4909 7.621796 TCTTTCTTTCTAACTAACCTCATCCC 58.378 38.462 0.00 0.00 0.00 3.85
4487 4910 9.503399 TTTCTTTCTTTCTAACTAACCTCATCC 57.497 33.333 0.00 0.00 0.00 3.51
4500 4923 9.712305 CACTGACTAGGATTTTCTTTCTTTCTA 57.288 33.333 0.00 0.00 0.00 2.10
4501 4924 8.214364 ACACTGACTAGGATTTTCTTTCTTTCT 58.786 33.333 0.00 0.00 0.00 2.52
4502 4925 8.286097 CACACTGACTAGGATTTTCTTTCTTTC 58.714 37.037 0.00 0.00 0.00 2.62
4503 4926 7.775561 ACACACTGACTAGGATTTTCTTTCTTT 59.224 33.333 0.00 0.00 0.00 2.52
4504 4927 7.283329 ACACACTGACTAGGATTTTCTTTCTT 58.717 34.615 0.00 0.00 0.00 2.52
4505 4928 6.831976 ACACACTGACTAGGATTTTCTTTCT 58.168 36.000 0.00 0.00 0.00 2.52
4506 4929 8.603242 TTACACACTGACTAGGATTTTCTTTC 57.397 34.615 0.00 0.00 0.00 2.62
4507 4930 9.574516 AATTACACACTGACTAGGATTTTCTTT 57.425 29.630 0.00 0.00 0.00 2.52
4508 4931 9.003658 CAATTACACACTGACTAGGATTTTCTT 57.996 33.333 0.00 0.00 0.00 2.52
4509 4932 7.119846 GCAATTACACACTGACTAGGATTTTCT 59.880 37.037 0.00 0.00 0.00 2.52
4510 4933 7.244192 GCAATTACACACTGACTAGGATTTTC 58.756 38.462 0.00 0.00 0.00 2.29
4511 4934 6.128282 CGCAATTACACACTGACTAGGATTTT 60.128 38.462 0.00 0.00 0.00 1.82
4512 4935 5.351465 CGCAATTACACACTGACTAGGATTT 59.649 40.000 0.00 0.00 0.00 2.17
4513 4936 4.870426 CGCAATTACACACTGACTAGGATT 59.130 41.667 0.00 0.00 0.00 3.01
4514 4937 4.081642 ACGCAATTACACACTGACTAGGAT 60.082 41.667 0.00 0.00 0.00 3.24
4515 4938 3.257375 ACGCAATTACACACTGACTAGGA 59.743 43.478 0.00 0.00 0.00 2.94
4516 4939 3.367932 CACGCAATTACACACTGACTAGG 59.632 47.826 0.00 0.00 0.00 3.02
4517 4940 3.987868 ACACGCAATTACACACTGACTAG 59.012 43.478 0.00 0.00 0.00 2.57
4518 4941 3.985008 ACACGCAATTACACACTGACTA 58.015 40.909 0.00 0.00 0.00 2.59
4519 4942 2.833794 ACACGCAATTACACACTGACT 58.166 42.857 0.00 0.00 0.00 3.41
4520 4943 4.210537 AGTTACACGCAATTACACACTGAC 59.789 41.667 0.00 0.00 0.00 3.51
4521 4944 4.373527 AGTTACACGCAATTACACACTGA 58.626 39.130 0.00 0.00 0.00 3.41
4522 4945 4.447724 AGAGTTACACGCAATTACACACTG 59.552 41.667 0.00 0.00 0.00 3.66
4523 4946 4.628074 AGAGTTACACGCAATTACACACT 58.372 39.130 0.00 0.00 0.00 3.55
4524 4947 4.985044 AGAGTTACACGCAATTACACAC 57.015 40.909 0.00 0.00 0.00 3.82
4525 4948 5.994887 AAAGAGTTACACGCAATTACACA 57.005 34.783 0.00 0.00 0.00 3.72
4526 4949 7.837923 CGTATAAAGAGTTACACGCAATTACAC 59.162 37.037 0.00 0.00 33.74 2.90
4527 4950 7.541783 ACGTATAAAGAGTTACACGCAATTACA 59.458 33.333 0.00 0.00 42.56 2.41
4528 4951 7.888727 ACGTATAAAGAGTTACACGCAATTAC 58.111 34.615 0.00 0.00 42.56 1.89
4529 4952 8.464770 AACGTATAAAGAGTTACACGCAATTA 57.535 30.769 0.00 0.00 42.56 1.40
4530 4953 6.956299 ACGTATAAAGAGTTACACGCAATT 57.044 33.333 0.00 0.00 42.56 2.32
4531 4954 6.956299 AACGTATAAAGAGTTACACGCAAT 57.044 33.333 0.00 0.00 42.56 3.56
4532 4955 6.768029 AAACGTATAAAGAGTTACACGCAA 57.232 33.333 0.00 0.00 42.56 4.85
4533 4956 6.033831 GCTAAACGTATAAAGAGTTACACGCA 59.966 38.462 0.00 0.00 42.56 5.24
4534 4957 6.033831 TGCTAAACGTATAAAGAGTTACACGC 59.966 38.462 0.00 0.00 42.56 5.34
4535 4958 7.496704 TGCTAAACGTATAAAGAGTTACACG 57.503 36.000 0.00 0.00 44.00 4.49


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

AutoCloner maintained by Alex Coulton.