Multiple sequence alignment - TraesCS4B01G083200

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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 TraesCS4B01G083200 chr4B 100.000 5851 0 0 1 5851 82023191 82017341 0.000000e+00 10805.0
1 TraesCS4B01G083200 chr4B 92.357 157 10 1 3943 4099 25944471 25944317 7.630000e-54 222.0
2 TraesCS4B01G083200 chr4A 94.413 3383 142 30 592 3947 542019914 542023276 0.000000e+00 5156.0
3 TraesCS4B01G083200 chr4A 90.789 912 36 19 4266 5146 542023541 542024435 0.000000e+00 1175.0
4 TraesCS4B01G083200 chr4A 89.533 535 39 8 29 560 542018841 542019361 0.000000e+00 662.0
5 TraesCS4B01G083200 chr4A 97.826 138 2 1 4070 4206 542023274 542023411 2.730000e-58 237.0
6 TraesCS4B01G083200 chr4A 87.730 163 12 6 5207 5365 542024561 542024719 3.600000e-42 183.0
7 TraesCS4B01G083200 chr4A 86.111 72 1 5 5407 5469 542024954 542025025 1.050000e-07 69.4
8 TraesCS4B01G083200 chr4D 95.495 2775 96 16 1178 3947 55068070 55065320 0.000000e+00 4405.0
9 TraesCS4B01G083200 chr4D 93.578 981 33 7 4072 5025 55065317 55064340 0.000000e+00 1435.0
10 TraesCS4B01G083200 chr4D 90.066 453 25 9 661 1107 55068625 55068187 2.370000e-158 569.0
11 TraesCS4B01G083200 chr4D 93.960 149 6 3 3931 4078 344231828 344231974 7.630000e-54 222.0
12 TraesCS4B01G083200 chr4D 80.365 219 27 10 5518 5735 55062827 55062624 1.020000e-32 152.0
13 TraesCS4B01G083200 chr4D 100.000 35 0 0 5817 5851 55062576 55062542 1.360000e-06 65.8
14 TraesCS4B01G083200 chr6B 93.710 2178 88 14 1798 3947 551033866 551031710 0.000000e+00 3217.0
15 TraesCS4B01G083200 chr6B 89.768 1036 55 18 796 1817 551035128 551034130 0.000000e+00 1279.0
16 TraesCS4B01G083200 chr6B 90.032 933 54 21 4069 4974 551031713 551030793 0.000000e+00 1171.0
17 TraesCS4B01G083200 chr6B 82.225 827 88 38 28 812 551036896 551036087 0.000000e+00 658.0
18 TraesCS4B01G083200 chr6B 76.815 854 168 20 3030 3860 717923341 717922495 2.490000e-123 453.0
19 TraesCS4B01G083200 chr6B 82.270 423 64 9 5439 5851 551030268 551029847 7.210000e-94 355.0
20 TraesCS4B01G083200 chr6B 73.724 666 154 13 3159 3819 717914135 717913486 2.110000e-59 241.0
21 TraesCS4B01G083200 chr6B 89.130 138 6 1 5052 5189 551030793 551030665 4.690000e-36 163.0
22 TraesCS4B01G083200 chr5B 87.741 2798 265 46 1178 3947 618121056 618123803 0.000000e+00 3195.0
23 TraesCS4B01G083200 chr5B 84.367 774 87 19 4131 4878 618123877 618124642 0.000000e+00 728.0
24 TraesCS4B01G083200 chr5B 93.431 137 8 1 979 1114 618120477 618120613 9.940000e-48 202.0
25 TraesCS4B01G083200 chr5A 87.996 2749 243 46 1219 3935 622986994 622989687 0.000000e+00 3168.0
26 TraesCS4B01G083200 chr5A 83.496 818 92 27 4069 4852 622989693 622990501 0.000000e+00 723.0
27 TraesCS4B01G083200 chr5A 96.947 131 4 0 979 1109 622986282 622986412 2.740000e-53 220.0
28 TraesCS4B01G083200 chr5D 90.370 1838 142 23 2116 3947 498623511 498625319 0.000000e+00 2381.0
29 TraesCS4B01G083200 chr5D 83.721 903 106 18 1213 2092 498622289 498623173 0.000000e+00 815.0
30 TraesCS4B01G083200 chr5D 83.475 823 89 26 4069 4852 498625316 498626130 0.000000e+00 723.0
31 TraesCS4B01G083200 chr5D 96.124 129 5 0 979 1107 498621662 498621790 1.650000e-50 211.0
32 TraesCS4B01G083200 chr2B 99.248 133 1 0 3939 4071 517436878 517437010 2.110000e-59 241.0
33 TraesCS4B01G083200 chr2B 81.124 249 37 10 300 543 442302722 442302479 2.150000e-44 191.0
34 TraesCS4B01G083200 chr3D 98.496 133 2 0 3944 4076 67064911 67064779 9.800000e-58 235.0
35 TraesCS4B01G083200 chr3D 93.960 149 6 3 3931 4078 411511487 411511633 7.630000e-54 222.0
36 TraesCS4B01G083200 chr1B 96.503 143 3 2 3943 4085 623397563 623397423 9.800000e-58 235.0
37 TraesCS4B01G083200 chr1A 97.778 135 3 0 3936 4070 505092527 505092393 3.530000e-57 233.0
38 TraesCS4B01G083200 chr1A 95.205 146 4 3 3925 4070 497228297 497228155 1.640000e-55 228.0
39 TraesCS4B01G083200 chr2D 93.960 149 7 2 3931 4078 592467971 592468118 2.120000e-54 224.0
40 TraesCS4B01G083200 chr6A 82.857 140 23 1 3296 3435 616991042 616991180 2.210000e-24 124.0
41 TraesCS4B01G083200 chr2A 77.622 143 27 5 5598 5737 530678151 530678291 1.350000e-11 82.4


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 TraesCS4B01G083200 chr4B 82017341 82023191 5850 True 10805.000000 10805 100.000000 1 5851 1 chr4B.!!$R2 5850
1 TraesCS4B01G083200 chr4A 542018841 542025025 6184 False 1247.066667 5156 91.067000 29 5469 6 chr4A.!!$F1 5440
2 TraesCS4B01G083200 chr4D 55062542 55068625 6083 True 1325.360000 4405 91.900800 661 5851 5 chr4D.!!$R1 5190
3 TraesCS4B01G083200 chr6B 551029847 551036896 7049 True 1140.500000 3217 87.855833 28 5851 6 chr6B.!!$R3 5823
4 TraesCS4B01G083200 chr6B 717922495 717923341 846 True 453.000000 453 76.815000 3030 3860 1 chr6B.!!$R2 830
5 TraesCS4B01G083200 chr6B 717913486 717914135 649 True 241.000000 241 73.724000 3159 3819 1 chr6B.!!$R1 660
6 TraesCS4B01G083200 chr5B 618120477 618124642 4165 False 1375.000000 3195 88.513000 979 4878 3 chr5B.!!$F1 3899
7 TraesCS4B01G083200 chr5A 622986282 622990501 4219 False 1370.333333 3168 89.479667 979 4852 3 chr5A.!!$F1 3873
8 TraesCS4B01G083200 chr5D 498621662 498626130 4468 False 1032.500000 2381 88.422500 979 4852 4 chr5D.!!$F1 3873

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
802 1368 0.773644 AATCCATCCCCCGAATCCTG 59.226 55.0 0.0 0.0 0.00 3.86 F
1420 3595 0.965866 TGCCTACAGACCCAGAGACG 60.966 60.0 0.0 0.0 0.00 4.18 F
2257 5066 0.973632 TTGTGATCCGTGCTGGTACT 59.026 50.0 0.0 0.0 39.52 2.73 F
3957 6821 0.526662 GCATATACTCCCTCCGTCCG 59.473 60.0 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2693 5530 0.107508 GGCTCATGGCTGCTGTAAGA 60.108 55.000 0.00 0.0 41.46 2.10 R
3027 5866 1.231641 CCACCACCCCACCTTCAAA 59.768 57.895 0.00 0.0 0.00 2.69 R
4047 6911 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.0 44.66 2.12 R
5752 9986 0.038526 CGTGAAGAACTAGGTGGCGT 60.039 55.000 0.00 0.0 0.00 5.68 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
21 22 4.164822 CACATGAAAGTTGCTTGTAGGG 57.835 45.455 0.00 0.00 0.00 3.53
22 23 2.558359 ACATGAAAGTTGCTTGTAGGGC 59.442 45.455 0.00 0.00 0.00 5.19
23 24 2.356665 TGAAAGTTGCTTGTAGGGCA 57.643 45.000 0.00 0.00 37.97 5.36
24 25 2.875296 TGAAAGTTGCTTGTAGGGCAT 58.125 42.857 0.00 0.00 39.54 4.40
25 26 2.557924 TGAAAGTTGCTTGTAGGGCATG 59.442 45.455 0.00 0.00 39.54 4.06
26 27 1.549203 AAGTTGCTTGTAGGGCATGG 58.451 50.000 0.00 0.00 39.54 3.66
55 56 6.094061 GCTTGTCTATCTTTAACTCTCACGT 58.906 40.000 0.00 0.00 0.00 4.49
60 61 2.400399 TCTTTAACTCTCACGTTGCCG 58.600 47.619 0.00 0.00 40.83 5.69
104 105 4.918037 ACCGTCTTTTATAGCTGTAGTCG 58.082 43.478 0.00 0.00 0.00 4.18
105 106 4.397417 ACCGTCTTTTATAGCTGTAGTCGT 59.603 41.667 0.00 0.00 0.00 4.34
175 177 5.640147 TGGGTTTCATTTGAGTAATGGAGT 58.360 37.500 0.00 0.00 43.19 3.85
177 179 5.163754 GGGTTTCATTTGAGTAATGGAGTCG 60.164 44.000 0.00 0.00 43.19 4.18
178 180 5.163754 GGTTTCATTTGAGTAATGGAGTCGG 60.164 44.000 0.00 0.00 43.19 4.79
332 342 7.851387 TTTGTAGATGTTTGTGTTAGTGTCA 57.149 32.000 0.00 0.00 0.00 3.58
335 345 5.991328 AGATGTTTGTGTTAGTGTCACAG 57.009 39.130 5.62 0.00 44.71 3.66
341 351 4.551702 TGTGTTAGTGTCACAGGCATAT 57.448 40.909 5.62 0.00 40.26 1.78
515 550 7.905604 ATGAACACATCGATTTTAGTTGAGA 57.094 32.000 0.00 0.00 0.00 3.27
518 553 8.229811 TGAACACATCGATTTTAGTTGAGATTG 58.770 33.333 0.00 0.00 0.00 2.67
612 1170 3.786866 AATCGATAGCCCCGGGGGT 62.787 63.158 43.90 43.90 46.51 4.95
802 1368 0.773644 AATCCATCCCCCGAATCCTG 59.226 55.000 0.00 0.00 0.00 3.86
817 1383 2.151502 TCCTGAACCCTAGAGCTCTG 57.848 55.000 26.78 15.29 0.00 3.35
842 2383 4.435970 TCCGCCACCTCTCGCCTA 62.436 66.667 0.00 0.00 0.00 3.93
871 2440 4.377760 TCCCTCGCCCTCGACCTT 62.378 66.667 0.00 0.00 40.21 3.50
904 2501 4.824515 CTCCCTCGCCCTCGACCT 62.825 72.222 0.00 0.00 40.21 3.85
905 2502 4.816984 TCCCTCGCCCTCGACCTC 62.817 72.222 0.00 0.00 40.21 3.85
988 2590 1.827399 AACTCCGTGGAAGATGGCGT 61.827 55.000 0.00 0.00 29.15 5.68
1126 2728 6.214208 CAGGTATCATCCATCATCTTCCCTTA 59.786 42.308 0.00 0.00 0.00 2.69
1152 2754 1.517832 CGCCACCTCCTTCCTACAG 59.482 63.158 0.00 0.00 0.00 2.74
1206 3380 6.442112 TGTTGATTTTGTTATTCATGTCGCA 58.558 32.000 0.00 0.00 0.00 5.10
1211 3385 7.811713 TGATTTTGTTATTCATGTCGCAATTCA 59.188 29.630 0.00 0.00 0.00 2.57
1420 3595 0.965866 TGCCTACAGACCCAGAGACG 60.966 60.000 0.00 0.00 0.00 4.18
1552 3731 4.469657 TGGCTTGATTCTGTTACCTTTGT 58.530 39.130 0.00 0.00 0.00 2.83
1579 3758 5.008019 GTCATGTGCATTCCTACGATGAAAT 59.992 40.000 0.00 0.00 0.00 2.17
1606 3785 6.122277 GTCATCCCTATTCCATTTGAACTCA 58.878 40.000 0.00 0.00 35.31 3.41
1659 3849 5.114780 TGAAGAAGATAATCAGCAGAGTGC 58.885 41.667 0.00 0.00 45.46 4.40
1706 3899 6.537301 TGTTTGGTAGAGTTTGTTCTACTGTG 59.463 38.462 11.62 0.00 45.67 3.66
1907 4389 5.194537 ACTGGGATTATTCATGACCCTCTTT 59.805 40.000 16.92 0.00 40.98 2.52
2003 4485 8.641541 ACAAACTGGACAAATCTCACATATTTT 58.358 29.630 0.00 0.00 0.00 1.82
2214 5023 5.942826 AGGAAAATCTTCTGAAGTGGCTAAG 59.057 40.000 16.43 0.00 0.00 2.18
2257 5066 0.973632 TTGTGATCCGTGCTGGTACT 59.026 50.000 0.00 0.00 39.52 2.73
2333 5142 5.842907 ACCAAAAGCAGGTACTTCATTTTC 58.157 37.500 0.00 0.00 37.67 2.29
2693 5530 6.699575 CTCCCGGTGAGAAATATTTGATTT 57.300 37.500 13.05 0.00 44.42 2.17
2852 5689 5.475719 TGATGTACGGACTGGAAAAGTAAG 58.524 41.667 0.00 0.00 40.07 2.34
2914 5751 3.847184 TGGAAATATGGGTGTGTCTGGTA 59.153 43.478 0.00 0.00 0.00 3.25
2991 5828 5.506317 GCACATCTTATTAGGTTGTCATGGC 60.506 44.000 0.00 0.00 0.00 4.40
3073 5912 9.094578 AGAGATGATAAGTATTTTGCTAGGCTA 57.905 33.333 0.00 0.00 0.00 3.93
3240 6079 0.618458 CAGCCTGCCAGGGTAAGTAA 59.382 55.000 16.38 0.00 45.88 2.24
3241 6080 1.004277 CAGCCTGCCAGGGTAAGTAAA 59.996 52.381 16.38 0.00 45.88 2.01
3799 6659 3.252974 ACGTTGATGATCTTGAGACCC 57.747 47.619 0.00 0.00 0.00 4.46
3914 6775 7.358435 CGTCGCTATCTGGTGATATTTACAAAG 60.358 40.741 0.00 0.00 34.95 2.77
3952 6816 9.495572 GCAATATAATAAGCATATACTCCCTCC 57.504 37.037 0.00 0.00 0.00 4.30
3953 6817 9.698309 CAATATAATAAGCATATACTCCCTCCG 57.302 37.037 0.00 0.00 0.00 4.63
3954 6818 9.435570 AATATAATAAGCATATACTCCCTCCGT 57.564 33.333 0.00 0.00 0.00 4.69
3955 6819 5.662674 AATAAGCATATACTCCCTCCGTC 57.337 43.478 0.00 0.00 0.00 4.79
3956 6820 1.926108 AGCATATACTCCCTCCGTCC 58.074 55.000 0.00 0.00 0.00 4.79
3957 6821 0.526662 GCATATACTCCCTCCGTCCG 59.473 60.000 0.00 0.00 0.00 4.79
3958 6822 1.885359 GCATATACTCCCTCCGTCCGA 60.885 57.143 0.00 0.00 0.00 4.55
3959 6823 2.511659 CATATACTCCCTCCGTCCGAA 58.488 52.381 0.00 0.00 0.00 4.30
3960 6824 2.734755 TATACTCCCTCCGTCCGAAA 57.265 50.000 0.00 0.00 0.00 3.46
3961 6825 1.856629 ATACTCCCTCCGTCCGAAAA 58.143 50.000 0.00 0.00 0.00 2.29
3962 6826 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
3963 6827 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
3964 6828 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
3965 6829 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
3966 6830 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
3967 6831 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3968 6832 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3969 6833 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3970 6834 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3971 6835 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
3972 6836 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
3973 6837 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
3974 6838 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
3975 6839 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
3976 6840 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
3977 6841 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
3978 6842 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
3979 6843 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
3980 6844 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
3981 6845 7.273381 CCGAAAATACTTGTCATCAAAATGGAC 59.727 37.037 0.00 0.00 33.42 4.02
3982 6846 7.807433 CGAAAATACTTGTCATCAAAATGGACA 59.193 33.333 0.00 0.00 33.42 4.02
3983 6847 9.474920 GAAAATACTTGTCATCAAAATGGACAA 57.525 29.630 0.00 0.00 34.59 3.18
3984 6848 9.829507 AAAATACTTGTCATCAAAATGGACAAA 57.170 25.926 7.70 0.00 34.98 2.83
3985 6849 9.829507 AAATACTTGTCATCAAAATGGACAAAA 57.170 25.926 7.70 0.84 34.98 2.44
3986 6850 9.829507 AATACTTGTCATCAAAATGGACAAAAA 57.170 25.926 7.70 0.55 34.98 1.94
3987 6851 7.775397 ACTTGTCATCAAAATGGACAAAAAG 57.225 32.000 7.70 0.11 34.98 2.27
3988 6852 7.555087 ACTTGTCATCAAAATGGACAAAAAGA 58.445 30.769 7.70 0.00 34.98 2.52
3989 6853 7.707893 ACTTGTCATCAAAATGGACAAAAAGAG 59.292 33.333 7.70 0.00 34.98 2.85
3990 6854 7.345422 TGTCATCAAAATGGACAAAAAGAGA 57.655 32.000 0.00 0.00 33.42 3.10
3991 6855 7.954835 TGTCATCAAAATGGACAAAAAGAGAT 58.045 30.769 0.00 0.00 33.42 2.75
3992 6856 7.868922 TGTCATCAAAATGGACAAAAAGAGATG 59.131 33.333 0.00 0.00 33.42 2.90
3993 6857 7.869429 GTCATCAAAATGGACAAAAAGAGATGT 59.131 33.333 0.00 0.00 33.42 3.06
3994 6858 9.076781 TCATCAAAATGGACAAAAAGAGATGTA 57.923 29.630 0.00 0.00 33.42 2.29
3995 6859 9.865321 CATCAAAATGGACAAAAAGAGATGTAT 57.135 29.630 0.00 0.00 0.00 2.29
3997 6861 9.300681 TCAAAATGGACAAAAAGAGATGTATCT 57.699 29.630 0.00 0.00 40.50 1.98
4002 6866 9.606631 ATGGACAAAAAGAGATGTATCTAGAAC 57.393 33.333 0.00 0.00 37.25 3.01
4003 6867 8.816894 TGGACAAAAAGAGATGTATCTAGAACT 58.183 33.333 0.00 0.00 37.25 3.01
4027 6891 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
4035 6899 9.170890 ACATCTAGATACATCCCCTTTTATTCA 57.829 33.333 4.54 0.00 0.00 2.57
4041 6905 9.713684 AGATACATCCCCTTTTATTCATTTTGA 57.286 29.630 0.00 0.00 0.00 2.69
4044 6908 8.378115 ACATCCCCTTTTATTCATTTTGATGA 57.622 30.769 0.00 0.00 32.39 2.92
4045 6909 8.260114 ACATCCCCTTTTATTCATTTTGATGAC 58.740 33.333 0.00 0.00 32.39 3.06
4046 6910 7.789202 TCCCCTTTTATTCATTTTGATGACA 57.211 32.000 0.00 0.00 0.00 3.58
4047 6911 8.200024 TCCCCTTTTATTCATTTTGATGACAA 57.800 30.769 0.00 0.00 0.00 3.18
4048 6912 8.313292 TCCCCTTTTATTCATTTTGATGACAAG 58.687 33.333 0.00 0.00 37.32 3.16
4049 6913 8.096414 CCCCTTTTATTCATTTTGATGACAAGT 58.904 33.333 0.00 0.00 37.32 3.16
4056 6920 8.915871 ATTCATTTTGATGACAAGTATTTCCG 57.084 30.769 0.00 0.00 37.32 4.30
4057 6921 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
4058 6922 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
4059 6923 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
4060 6924 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
4061 6925 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
4062 6926 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
4063 6927 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
4064 6928 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4065 6929 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4066 6930 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
4067 6931 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4124 6998 2.085320 ACTCGAACGTAGATGCTCAGT 58.915 47.619 0.00 0.00 0.00 3.41
4201 7087 8.182227 GCATGGACTTAGTAGTTGAAATTAACC 58.818 37.037 0.00 0.00 33.84 2.85
4263 7154 7.415653 CCCTTGTAATTCAGTAGAGCCAAAATC 60.416 40.741 0.00 0.00 0.00 2.17
4291 7252 3.937079 GGTTTACCACGGATGAACTAAGG 59.063 47.826 0.00 0.00 35.64 2.69
4391 7352 1.188863 GGTCCTTCAATGGCAAGCAT 58.811 50.000 0.00 0.00 0.00 3.79
4700 7717 1.896660 GGTCGCCAAGTGGAAGCAA 60.897 57.895 0.18 0.00 37.39 3.91
4866 7885 2.551459 GAGTGAATGCTGCTGAGTGTTT 59.449 45.455 0.00 0.00 0.00 2.83
4886 7905 0.307760 GTTTTCTGCCTGTCGTGTGG 59.692 55.000 0.00 0.00 0.00 4.17
4895 7914 0.514255 CTGTCGTGTGGATTGCTGTG 59.486 55.000 0.00 0.00 0.00 3.66
4906 7925 2.070783 GATTGCTGTGGTTTTGCATGG 58.929 47.619 0.00 0.00 36.55 3.66
4915 7934 1.745653 GGTTTTGCATGGTAGGCTCTC 59.254 52.381 0.00 0.00 0.00 3.20
4916 7935 1.745653 GTTTTGCATGGTAGGCTCTCC 59.254 52.381 0.00 0.00 0.00 3.71
4928 7947 1.686052 AGGCTCTCCTTAGATCAAGCG 59.314 52.381 0.00 0.00 40.66 4.68
4995 8018 8.091385 TGATCATGTTTATGGAGATCGATTTG 57.909 34.615 0.00 0.00 38.28 2.32
4996 8019 6.304356 TCATGTTTATGGAGATCGATTTGC 57.696 37.500 0.00 0.00 34.97 3.68
4997 8020 5.821995 TCATGTTTATGGAGATCGATTTGCA 59.178 36.000 12.46 12.46 34.97 4.08
4998 8021 6.318396 TCATGTTTATGGAGATCGATTTGCAA 59.682 34.615 13.99 0.00 34.97 4.08
4999 8022 6.507958 TGTTTATGGAGATCGATTTGCAAA 57.492 33.333 15.44 15.44 0.00 3.68
5001 8024 6.974048 TGTTTATGGAGATCGATTTGCAAATG 59.026 34.615 28.67 19.29 0.00 2.32
5002 8025 6.698008 TTATGGAGATCGATTTGCAAATGT 57.302 33.333 28.67 14.22 0.00 2.71
5003 8026 4.359971 TGGAGATCGATTTGCAAATGTG 57.640 40.909 28.67 19.61 0.00 3.21
5004 8027 3.129113 TGGAGATCGATTTGCAAATGTGG 59.871 43.478 28.67 16.75 0.00 4.17
5028 8051 4.401022 TGGAATGCTGGTCATCATAATCC 58.599 43.478 0.00 0.00 33.40 3.01
5031 8054 3.497103 TGCTGGTCATCATAATCCCTG 57.503 47.619 0.00 0.00 0.00 4.45
5038 8061 4.037208 GGTCATCATAATCCCTGTTTGCAG 59.963 45.833 0.00 0.00 42.22 4.41
5086 8960 4.530161 AGCTGTACTGGAATCACTTCTCTT 59.470 41.667 1.65 0.00 0.00 2.85
5087 8961 5.717178 AGCTGTACTGGAATCACTTCTCTTA 59.283 40.000 1.65 0.00 0.00 2.10
5088 8962 6.039616 GCTGTACTGGAATCACTTCTCTTAG 58.960 44.000 1.65 0.00 0.00 2.18
5089 8963 6.350612 GCTGTACTGGAATCACTTCTCTTAGT 60.351 42.308 1.65 0.00 0.00 2.24
5090 8964 7.540474 TGTACTGGAATCACTTCTCTTAGTT 57.460 36.000 0.00 0.00 0.00 2.24
5091 8965 7.603651 TGTACTGGAATCACTTCTCTTAGTTC 58.396 38.462 0.00 0.00 0.00 3.01
5092 8966 6.926630 ACTGGAATCACTTCTCTTAGTTCT 57.073 37.500 0.00 0.00 0.00 3.01
5093 8967 7.309770 ACTGGAATCACTTCTCTTAGTTCTT 57.690 36.000 0.00 0.00 0.00 2.52
5094 8968 7.740805 ACTGGAATCACTTCTCTTAGTTCTTT 58.259 34.615 0.00 0.00 0.00 2.52
5120 8994 1.202065 CGTCGGATTTTGCACATCAGG 60.202 52.381 7.26 0.02 0.00 3.86
5140 9014 3.522750 AGGCAGACAGGAAGAGATGAAAT 59.477 43.478 0.00 0.00 0.00 2.17
5147 9021 8.828644 CAGACAGGAAGAGATGAAATTAATCAG 58.171 37.037 0.00 0.00 31.76 2.90
5177 9097 0.758123 AACCAAGCACCCCAATGTTG 59.242 50.000 0.00 0.00 0.00 3.33
5201 9121 9.853555 TTGGAATCATAACAATCATAACACAAC 57.146 29.630 0.00 0.00 0.00 3.32
5212 9132 5.175090 TCATAACACAACGTTGAAATGCA 57.825 34.783 33.66 13.64 38.63 3.96
5213 9133 5.767269 TCATAACACAACGTTGAAATGCAT 58.233 33.333 33.66 16.00 38.63 3.96
5214 9134 5.855925 TCATAACACAACGTTGAAATGCATC 59.144 36.000 33.66 0.00 38.63 3.91
5215 9135 3.706802 ACACAACGTTGAAATGCATCA 57.293 38.095 33.66 0.00 0.00 3.07
5217 9137 4.229096 ACACAACGTTGAAATGCATCATC 58.771 39.130 33.66 2.27 0.00 2.92
5219 9139 4.860352 CACAACGTTGAAATGCATCATCAT 59.140 37.500 33.66 3.81 0.00 2.45
5221 9141 5.927689 ACAACGTTGAAATGCATCATCATTT 59.072 32.000 33.66 2.72 46.06 2.32
5222 9142 6.424509 ACAACGTTGAAATGCATCATCATTTT 59.575 30.769 33.66 2.35 44.15 1.82
5223 9143 7.598118 ACAACGTTGAAATGCATCATCATTTTA 59.402 29.630 33.66 0.00 44.15 1.52
5226 9146 9.454585 ACGTTGAAATGCATCATCATTTTATAG 57.545 29.630 13.95 5.79 44.15 1.31
5366 9314 6.486993 AGGTCTTTGATTTGACTAGTGAAACC 59.513 38.462 9.80 0.36 33.41 3.27
5371 9319 4.515191 TGATTTGACTAGTGAAACCTGTGC 59.485 41.667 9.80 0.00 37.80 4.57
5390 9511 4.133078 GTGCAATTTCCAACCCATTGAAA 58.867 39.130 0.00 0.00 38.15 2.69
5403 9524 3.937706 CCCATTGAAACAAGCACAAACAA 59.062 39.130 0.00 0.00 0.00 2.83
5437 9596 8.474006 ACAACCAAACAGAATTTAACAAGTTC 57.526 30.769 0.00 0.00 0.00 3.01
5471 9642 3.486653 ACTAAACTAGGCCAGGTACCT 57.513 47.619 9.21 9.21 41.57 3.08
5505 9685 3.211963 GCATGGCCACCGACATCC 61.212 66.667 8.16 0.00 0.00 3.51
5524 9757 1.015085 CCCGTCGTTATTGGCGTTGA 61.015 55.000 0.00 0.00 0.00 3.18
5594 9828 1.538047 GCATCCTTCACTCCTTTGCA 58.462 50.000 0.00 0.00 0.00 4.08
5627 9861 1.809869 CGACTCGGATGAAGAGGCA 59.190 57.895 0.00 0.00 43.77 4.75
5631 9865 2.202932 CGGATGAAGAGGCACGGG 60.203 66.667 0.00 0.00 0.00 5.28
5655 9889 2.108278 CTCCGTCGGACCCACCTTTT 62.108 60.000 10.71 0.00 36.31 2.27
5676 9910 0.460987 GGAGCTGGTCATTGAGTCGG 60.461 60.000 9.30 0.00 0.00 4.79
5677 9911 0.247736 GAGCTGGTCATTGAGTCGGT 59.752 55.000 1.28 0.00 0.00 4.69
5682 9916 1.623311 TGGTCATTGAGTCGGTGTCAT 59.377 47.619 0.00 0.00 0.00 3.06
5685 9919 3.325870 GTCATTGAGTCGGTGTCATTGA 58.674 45.455 0.00 0.00 33.85 2.57
5689 9923 0.242825 GAGTCGGTGTCATTGACGGA 59.757 55.000 11.97 6.62 37.69 4.69
5768 10002 1.439679 CCAACGCCACCTAGTTCTTC 58.560 55.000 0.00 0.00 0.00 2.87
5770 10004 1.798813 CAACGCCACCTAGTTCTTCAC 59.201 52.381 0.00 0.00 0.00 3.18
5791 10025 2.202388 CGCTTCATGCACGCCTTG 60.202 61.111 0.00 0.00 43.06 3.61
5808 10042 2.029964 GGCCACGACTTTGGACGA 59.970 61.111 0.00 0.00 39.24 4.20
5812 10046 0.388649 CCACGACTTTGGACGAGGAG 60.389 60.000 0.00 0.00 41.58 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.612479 GCCCTACAAGCAACTTTCATGTG 60.612 47.826 0.00 0.00 0.00 3.21
1 2 2.558359 GCCCTACAAGCAACTTTCATGT 59.442 45.455 0.00 0.00 0.00 3.21
2 3 2.557924 TGCCCTACAAGCAACTTTCATG 59.442 45.455 0.00 0.00 37.28 3.07
3 4 2.875296 TGCCCTACAAGCAACTTTCAT 58.125 42.857 0.00 0.00 37.28 2.57
4 5 2.356665 TGCCCTACAAGCAACTTTCA 57.643 45.000 0.00 0.00 37.28 2.69
5 6 2.094545 CCATGCCCTACAAGCAACTTTC 60.095 50.000 0.00 0.00 44.83 2.62
6 7 1.895131 CCATGCCCTACAAGCAACTTT 59.105 47.619 0.00 0.00 44.83 2.66
7 8 1.203050 ACCATGCCCTACAAGCAACTT 60.203 47.619 0.00 0.00 44.83 2.66
8 9 0.405585 ACCATGCCCTACAAGCAACT 59.594 50.000 0.00 0.00 44.83 3.16
9 10 0.527565 CACCATGCCCTACAAGCAAC 59.472 55.000 0.00 0.00 44.83 4.17
10 11 0.112218 ACACCATGCCCTACAAGCAA 59.888 50.000 0.00 0.00 44.83 3.91
11 12 0.112218 AACACCATGCCCTACAAGCA 59.888 50.000 0.00 0.00 45.94 3.91
12 13 0.527565 CAACACCATGCCCTACAAGC 59.472 55.000 0.00 0.00 0.00 4.01
13 14 0.527565 GCAACACCATGCCCTACAAG 59.472 55.000 0.00 0.00 40.49 3.16
14 15 2.652313 GCAACACCATGCCCTACAA 58.348 52.632 0.00 0.00 40.49 2.41
15 16 4.413928 GCAACACCATGCCCTACA 57.586 55.556 0.00 0.00 40.49 2.74
21 22 3.012518 AGATAGACAAGCAACACCATGC 58.987 45.455 0.00 0.00 46.78 4.06
22 23 5.633830 AAAGATAGACAAGCAACACCATG 57.366 39.130 0.00 0.00 0.00 3.66
23 24 6.942576 AGTTAAAGATAGACAAGCAACACCAT 59.057 34.615 0.00 0.00 0.00 3.55
24 25 6.296026 AGTTAAAGATAGACAAGCAACACCA 58.704 36.000 0.00 0.00 0.00 4.17
25 26 6.651225 AGAGTTAAAGATAGACAAGCAACACC 59.349 38.462 0.00 0.00 0.00 4.16
26 27 7.385205 TGAGAGTTAAAGATAGACAAGCAACAC 59.615 37.037 0.00 0.00 0.00 3.32
55 56 2.785562 ACCTACAAGCATAAACGGCAA 58.214 42.857 0.00 0.00 0.00 4.52
104 105 7.657761 TCAGAGGAACAGTTCAAGAGATAAAAC 59.342 37.037 15.36 0.00 0.00 2.43
105 106 7.735917 TCAGAGGAACAGTTCAAGAGATAAAA 58.264 34.615 15.36 0.00 0.00 1.52
208 210 3.692101 TCCACGCATTTTTCGTCCATATT 59.308 39.130 0.00 0.00 38.19 1.28
311 321 6.073765 CCTGTGACACTAACACAAACATCTAC 60.074 42.308 7.20 0.00 45.49 2.59
332 342 9.195411 CGCATAAAAATTATCAAATATGCCTGT 57.805 29.630 9.27 0.00 32.96 4.00
341 351 7.008810 GCTCCGTTTCGCATAAAAATTATCAAA 59.991 33.333 0.00 0.00 0.00 2.69
525 560 7.372918 CACGTGCGAAAAATGATTTTTGAAATT 59.627 29.630 19.47 0.00 42.51 1.82
612 1170 4.752879 GTGCTCCACGGCCGCTAA 62.753 66.667 28.58 9.67 0.00 3.09
664 1223 1.208358 GTTTTAAGCGTGGGTCGGC 59.792 57.895 0.00 0.00 40.26 5.54
778 1341 4.643387 CGGGGGATGGATTCGGCC 62.643 72.222 0.00 0.00 0.00 6.13
802 1368 0.179086 GCTGCAGAGCTCTAGGGTTC 60.179 60.000 20.43 0.00 42.52 3.62
988 2590 2.170397 TGGCTTCCATCGAGATTGCTAA 59.830 45.455 0.00 0.00 0.00 3.09
1093 2695 7.850419 AGATGATGGATGATACCTGAGGATATT 59.150 37.037 4.99 0.00 0.00 1.28
1152 2754 1.136500 CTCCTACCTACTTTGACCGCC 59.864 57.143 0.00 0.00 0.00 6.13
1206 3380 4.802039 GTCGCTGCAAATCATGATTGAATT 59.198 37.500 21.39 3.06 34.96 2.17
1211 3385 2.009051 TCGTCGCTGCAAATCATGATT 58.991 42.857 15.36 15.36 0.00 2.57
1420 3595 1.208293 CAGTAGCCCTGGGTCTTCTTC 59.792 57.143 15.56 0.62 37.54 2.87
1552 3731 4.729227 TCGTAGGAATGCACATGACTTA 57.271 40.909 0.00 0.00 0.00 2.24
1606 3785 6.367969 CACGTACAAAAGTTAAGCAGGATAGT 59.632 38.462 0.00 0.00 0.00 2.12
1659 3849 3.389925 AGGTGTTTCCATGCATGTTTG 57.610 42.857 24.58 10.30 39.02 2.93
1706 3899 9.974980 TTTCTACAGAAAAATCCCAACAATTAC 57.025 29.630 1.92 0.00 40.68 1.89
1788 3983 9.517609 GGTCATAACAGTAGAACACTATAACAG 57.482 37.037 0.00 0.00 34.98 3.16
1827 4307 3.513515 TGGAGTTAAATTTGGATGGGCAC 59.486 43.478 0.00 0.00 0.00 5.01
1868 4348 6.610075 AATCCCAGTAACAGAATGCAAAAT 57.390 33.333 0.00 0.00 42.53 1.82
1907 4389 9.076781 TGTCAAATAATCCTCTTTCAATCAACA 57.923 29.630 0.00 0.00 0.00 3.33
1970 4452 2.719531 TTGTCCAGTTTGTAGCCACA 57.280 45.000 0.00 0.00 0.00 4.17
2168 4977 7.053498 TCCTGCAACACATACACATATAACAT 58.947 34.615 0.00 0.00 0.00 2.71
2181 4990 4.828939 TCAGAAGATTTTCCTGCAACACAT 59.171 37.500 0.00 0.00 33.64 3.21
2214 5023 4.040217 ACTGATCTCTGGCCTTATCATCAC 59.960 45.833 3.32 0.00 0.00 3.06
2257 5066 3.823281 TTCCAGTACACTTCCGTGAAA 57.177 42.857 0.00 0.00 43.97 2.69
2295 5104 0.602638 TTGGTACACAAGCTCAGGCG 60.603 55.000 0.00 0.00 40.79 5.52
2693 5530 0.107508 GGCTCATGGCTGCTGTAAGA 60.108 55.000 0.00 0.00 41.46 2.10
2852 5689 1.377333 CTTCCCTTGAACTCCCGCC 60.377 63.158 0.00 0.00 0.00 6.13
2914 5751 4.166725 TCACCTGAAGATAGGCCATGAAAT 59.833 41.667 5.01 0.00 41.75 2.17
3027 5866 1.231641 CCACCACCCCACCTTCAAA 59.768 57.895 0.00 0.00 0.00 2.69
3028 5867 1.289982 TTCCACCACCCCACCTTCAA 61.290 55.000 0.00 0.00 0.00 2.69
3109 5948 7.731054 AGGACTTCTTATCAATAAGAGCGAAT 58.269 34.615 11.26 0.11 46.56 3.34
3240 6079 6.901081 AAAGAGGTAGCAGTAGCAATTTTT 57.099 33.333 0.00 0.00 45.49 1.94
3241 6080 6.901081 AAAAGAGGTAGCAGTAGCAATTTT 57.099 33.333 0.00 0.00 45.49 1.82
3307 6163 3.941483 ACAAGACTCACCTTTCAACACAG 59.059 43.478 0.00 0.00 0.00 3.66
3799 6659 1.813513 AAATGTTCTCCTGTCGCCAG 58.186 50.000 0.00 0.00 38.50 4.85
3932 6796 5.655532 GGACGGAGGGAGTATATGCTTATTA 59.344 44.000 0.00 0.00 0.00 0.98
3933 6797 4.466726 GGACGGAGGGAGTATATGCTTATT 59.533 45.833 0.00 0.00 0.00 1.40
3935 6799 3.428532 GGACGGAGGGAGTATATGCTTA 58.571 50.000 0.00 0.00 0.00 3.09
3937 6801 1.887088 CGGACGGAGGGAGTATATGCT 60.887 57.143 0.00 0.00 0.00 3.79
3938 6802 0.526662 CGGACGGAGGGAGTATATGC 59.473 60.000 0.00 0.00 0.00 3.14
3939 6803 2.195741 TCGGACGGAGGGAGTATATG 57.804 55.000 0.00 0.00 0.00 1.78
3941 6805 2.734755 TTTCGGACGGAGGGAGTATA 57.265 50.000 0.00 0.00 0.00 1.47
3942 6806 1.856629 TTTTCGGACGGAGGGAGTAT 58.143 50.000 0.00 0.00 0.00 2.12
3943 6807 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
3944 6808 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
3945 6809 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
3946 6810 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
3947 6811 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3948 6812 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3949 6813 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
3950 6814 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
3951 6815 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
3952 6816 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
3953 6817 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
3954 6818 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
3955 6819 7.273381 GTCCATTTTGATGACAAGTATTTTCGG 59.727 37.037 0.00 0.00 37.32 4.30
3956 6820 7.807433 TGTCCATTTTGATGACAAGTATTTTCG 59.193 33.333 0.00 0.00 37.32 3.46
3957 6821 9.474920 TTGTCCATTTTGATGACAAGTATTTTC 57.525 29.630 0.00 0.00 37.32 2.29
3958 6822 9.829507 TTTGTCCATTTTGATGACAAGTATTTT 57.170 25.926 0.00 0.00 37.13 1.82
3959 6823 9.829507 TTTTGTCCATTTTGATGACAAGTATTT 57.170 25.926 0.00 0.00 37.13 1.40
3960 6824 9.829507 TTTTTGTCCATTTTGATGACAAGTATT 57.170 25.926 0.00 0.00 37.13 1.89
3961 6825 9.480053 CTTTTTGTCCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.13 2.12
3962 6826 8.690884 TCTTTTTGTCCATTTTGATGACAAGTA 58.309 29.630 0.00 0.00 37.13 2.24
3963 6827 7.555087 TCTTTTTGTCCATTTTGATGACAAGT 58.445 30.769 0.00 0.00 37.13 3.16
3964 6828 7.922278 TCTCTTTTTGTCCATTTTGATGACAAG 59.078 33.333 0.00 0.00 37.13 3.16
3965 6829 7.780064 TCTCTTTTTGTCCATTTTGATGACAA 58.220 30.769 0.00 0.00 34.47 3.18
3966 6830 7.345422 TCTCTTTTTGTCCATTTTGATGACA 57.655 32.000 0.00 0.00 0.00 3.58
3967 6831 7.869429 ACATCTCTTTTTGTCCATTTTGATGAC 59.131 33.333 0.00 0.00 33.85 3.06
3968 6832 7.954835 ACATCTCTTTTTGTCCATTTTGATGA 58.045 30.769 0.00 0.00 33.85 2.92
3969 6833 9.865321 ATACATCTCTTTTTGTCCATTTTGATG 57.135 29.630 0.00 0.00 35.23 3.07
3971 6835 9.300681 AGATACATCTCTTTTTGTCCATTTTGA 57.699 29.630 0.00 0.00 29.30 2.69
3976 6840 9.606631 GTTCTAGATACATCTCTTTTTGTCCAT 57.393 33.333 0.00 0.00 38.32 3.41
3977 6841 8.816894 AGTTCTAGATACATCTCTTTTTGTCCA 58.183 33.333 0.00 0.00 38.32 4.02
4001 6865 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
4009 6873 9.170890 TGAATAAAAGGGGATGTATCTAGATGT 57.829 33.333 15.79 1.25 0.00 3.06
4015 6879 9.713684 TCAAAATGAATAAAAGGGGATGTATCT 57.286 29.630 0.00 0.00 0.00 1.98
4018 6882 9.486123 TCATCAAAATGAATAAAAGGGGATGTA 57.514 29.630 0.00 0.00 38.97 2.29
4019 6883 8.260114 GTCATCAAAATGAATAAAAGGGGATGT 58.740 33.333 0.00 0.00 43.42 3.06
4020 6884 8.259411 TGTCATCAAAATGAATAAAAGGGGATG 58.741 33.333 0.00 0.00 43.42 3.51
4021 6885 8.378115 TGTCATCAAAATGAATAAAAGGGGAT 57.622 30.769 0.00 0.00 43.42 3.85
4022 6886 7.789202 TGTCATCAAAATGAATAAAAGGGGA 57.211 32.000 0.00 0.00 43.42 4.81
4023 6887 8.096414 ACTTGTCATCAAAATGAATAAAAGGGG 58.904 33.333 0.00 0.00 43.42 4.79
4031 6895 7.975616 CCGGAAATACTTGTCATCAAAATGAAT 59.024 33.333 0.00 0.00 43.42 2.57
4032 6896 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
4033 6897 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
4034 6898 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
4035 6899 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
4036 6900 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
4037 6901 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
4038 6902 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
4039 6903 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
4040 6904 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
4041 6905 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
4042 6906 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
4043 6907 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4044 6908 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4045 6909 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4046 6910 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
4047 6911 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
4048 6912 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
4049 6913 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
4050 6914 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
4051 6915 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
4052 6916 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
4053 6917 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
4054 6918 2.119655 CAGTACTCCCTCCGTCCGG 61.120 68.421 0.00 0.00 0.00 5.14
4055 6919 0.679002 TTCAGTACTCCCTCCGTCCG 60.679 60.000 0.00 0.00 0.00 4.79
4056 6920 1.777941 ATTCAGTACTCCCTCCGTCC 58.222 55.000 0.00 0.00 0.00 4.79
4057 6921 2.885894 CCTATTCAGTACTCCCTCCGTC 59.114 54.545 0.00 0.00 0.00 4.79
4058 6922 2.244252 ACCTATTCAGTACTCCCTCCGT 59.756 50.000 0.00 0.00 0.00 4.69
4059 6923 2.946785 ACCTATTCAGTACTCCCTCCG 58.053 52.381 0.00 0.00 0.00 4.63
4060 6924 5.206587 TGTAACCTATTCAGTACTCCCTCC 58.793 45.833 0.00 0.00 0.00 4.30
4061 6925 5.302313 CCTGTAACCTATTCAGTACTCCCTC 59.698 48.000 0.00 0.00 0.00 4.30
4062 6926 5.043582 TCCTGTAACCTATTCAGTACTCCCT 60.044 44.000 0.00 0.00 0.00 4.20
4063 6927 5.206587 TCCTGTAACCTATTCAGTACTCCC 58.793 45.833 0.00 0.00 0.00 4.30
4064 6928 6.786967 TTCCTGTAACCTATTCAGTACTCC 57.213 41.667 0.00 0.00 0.00 3.85
4124 6998 9.883142 ACAGGTGAAGACAATTAAAAATTTCAA 57.117 25.926 0.00 0.00 0.00 2.69
4230 7116 8.150945 GCTCTACTGAATTACAAGGGAATCATA 58.849 37.037 0.00 0.00 0.00 2.15
4304 7265 3.451526 TGCGAGATATCTGAACAAGCAG 58.548 45.455 10.74 0.00 37.24 4.24
4526 7543 2.707849 GGGAGTAAGCAGCGACGGA 61.708 63.158 0.00 0.00 0.00 4.69
4700 7717 2.182791 CGCTCATCCTCGTGCAGT 59.817 61.111 0.00 0.00 0.00 4.40
4852 7869 2.754552 AGAAAACAAACACTCAGCAGCA 59.245 40.909 0.00 0.00 0.00 4.41
4866 7885 1.013596 CACACGACAGGCAGAAAACA 58.986 50.000 0.00 0.00 0.00 2.83
4886 7905 2.070783 CCATGCAAAACCACAGCAATC 58.929 47.619 0.00 0.00 42.15 2.67
4895 7914 1.745653 GAGAGCCTACCATGCAAAACC 59.254 52.381 0.00 0.00 0.00 3.27
4906 7925 3.305064 CGCTTGATCTAAGGAGAGCCTAC 60.305 52.174 0.00 0.00 46.28 3.18
4915 7934 4.371786 TCAACTATGCGCTTGATCTAAGG 58.628 43.478 9.73 0.00 36.87 2.69
4916 7935 6.150738 GATCAACTATGCGCTTGATCTAAG 57.849 41.667 28.88 12.80 44.99 2.18
4928 7947 6.980978 TGCACTACTAGAAAGATCAACTATGC 59.019 38.462 0.00 3.50 0.00 3.14
4970 7993 7.308169 GCAAATCGATCTCCATAAACATGATCA 60.308 37.037 0.00 0.00 34.80 2.92
4995 8018 2.070783 CAGCATTCCAACCACATTTGC 58.929 47.619 0.00 0.00 0.00 3.68
4996 8019 2.037511 ACCAGCATTCCAACCACATTTG 59.962 45.455 0.00 0.00 0.00 2.32
4997 8020 2.299867 GACCAGCATTCCAACCACATTT 59.700 45.455 0.00 0.00 0.00 2.32
4998 8021 1.895131 GACCAGCATTCCAACCACATT 59.105 47.619 0.00 0.00 0.00 2.71
4999 8022 1.203038 TGACCAGCATTCCAACCACAT 60.203 47.619 0.00 0.00 0.00 3.21
5001 8024 1.474077 GATGACCAGCATTCCAACCAC 59.526 52.381 0.00 0.00 37.34 4.16
5002 8025 1.075212 TGATGACCAGCATTCCAACCA 59.925 47.619 0.00 0.00 37.34 3.67
5003 8026 1.838112 TGATGACCAGCATTCCAACC 58.162 50.000 0.00 0.00 37.34 3.77
5004 8027 5.278660 GGATTATGATGACCAGCATTCCAAC 60.279 44.000 6.06 0.00 38.52 3.77
5028 8051 2.884012 TGTAACCACATCTGCAAACAGG 59.116 45.455 0.00 0.00 44.59 4.00
5031 8054 6.843069 AAAAATGTAACCACATCTGCAAAC 57.157 33.333 0.00 0.00 44.83 2.93
5086 8960 8.545420 GCAAAATCCGACGATAATAAAGAACTA 58.455 33.333 0.00 0.00 0.00 2.24
5087 8961 7.065324 TGCAAAATCCGACGATAATAAAGAACT 59.935 33.333 0.00 0.00 0.00 3.01
5088 8962 7.163682 GTGCAAAATCCGACGATAATAAAGAAC 59.836 37.037 0.00 0.00 0.00 3.01
5089 8963 7.148390 TGTGCAAAATCCGACGATAATAAAGAA 60.148 33.333 0.00 0.00 0.00 2.52
5090 8964 6.314152 TGTGCAAAATCCGACGATAATAAAGA 59.686 34.615 0.00 0.00 0.00 2.52
5091 8965 6.482835 TGTGCAAAATCCGACGATAATAAAG 58.517 36.000 0.00 0.00 0.00 1.85
5092 8966 6.424176 TGTGCAAAATCCGACGATAATAAA 57.576 33.333 0.00 0.00 0.00 1.40
5093 8967 6.258947 TGATGTGCAAAATCCGACGATAATAA 59.741 34.615 0.00 0.00 25.63 1.40
5094 8968 5.755861 TGATGTGCAAAATCCGACGATAATA 59.244 36.000 0.00 0.00 25.63 0.98
5120 8994 6.992063 TTAATTTCATCTCTTCCTGTCTGC 57.008 37.500 0.00 0.00 0.00 4.26
5177 9097 8.181573 ACGTTGTGTTATGATTGTTATGATTCC 58.818 33.333 0.00 0.00 0.00 3.01
5189 9109 5.767269 TGCATTTCAACGTTGTGTTATGAT 58.233 33.333 26.47 9.33 39.29 2.45
5190 9110 5.175090 TGCATTTCAACGTTGTGTTATGA 57.825 34.783 26.47 3.83 39.29 2.15
5191 9111 5.628606 TGATGCATTTCAACGTTGTGTTATG 59.371 36.000 26.47 22.44 39.29 1.90
5192 9112 5.767269 TGATGCATTTCAACGTTGTGTTAT 58.233 33.333 26.47 15.61 39.29 1.89
5193 9113 5.175090 TGATGCATTTCAACGTTGTGTTA 57.825 34.783 26.47 12.10 39.29 2.41
5194 9114 4.039151 TGATGCATTTCAACGTTGTGTT 57.961 36.364 26.47 10.47 43.09 3.32
5195 9115 3.706802 TGATGCATTTCAACGTTGTGT 57.293 38.095 26.47 11.83 0.00 3.72
5196 9116 4.228317 TGATGATGCATTTCAACGTTGTG 58.772 39.130 26.47 18.68 0.00 3.33
5197 9117 4.502171 TGATGATGCATTTCAACGTTGT 57.498 36.364 26.47 6.60 0.00 3.32
5201 9121 9.667989 TCTATAAAATGATGATGCATTTCAACG 57.332 29.630 14.84 0.00 45.09 4.10
5276 9221 9.688091 TTTTAGAGCCAACCACAATACATTATA 57.312 29.630 0.00 0.00 0.00 0.98
5288 9233 4.522789 GTGGAAGATTTTTAGAGCCAACCA 59.477 41.667 0.00 0.00 0.00 3.67
5294 9239 5.818336 GGGAGTAGTGGAAGATTTTTAGAGC 59.182 44.000 0.00 0.00 0.00 4.09
5366 9314 3.068560 CAATGGGTTGGAAATTGCACAG 58.931 45.455 0.00 0.00 0.00 3.66
5371 9319 5.277925 GCTTGTTTCAATGGGTTGGAAATTG 60.278 40.000 0.00 0.00 34.66 2.32
5390 9511 9.458374 GTTGTAAATATAGTTGTTTGTGCTTGT 57.542 29.630 0.00 0.00 0.00 3.16
5437 9596 8.235226 GGCCTAGTTTAGTTAGCTTTTAGTTTG 58.765 37.037 0.00 0.00 0.00 2.93
5487 9658 2.124570 GATGTCGGTGGCCATGCT 60.125 61.111 9.72 0.00 0.00 3.79
5505 9685 1.015085 TCAACGCCAATAACGACGGG 61.015 55.000 0.00 0.00 0.00 5.28
5513 9693 2.418368 AGGATGCTTCAACGCCAATA 57.582 45.000 1.64 0.00 0.00 1.90
5516 9696 1.448985 GTAAGGATGCTTCAACGCCA 58.551 50.000 1.37 0.00 0.00 5.69
5524 9757 2.305607 TGGCCGGGTAAGGATGCTT 61.306 57.895 2.18 4.41 0.00 3.91
5549 9782 4.377708 ATCTGCACCACGAGCGCA 62.378 61.111 11.47 0.00 33.85 6.09
5582 9815 3.141398 GACAAGTGATGCAAAGGAGTGA 58.859 45.455 0.00 0.00 0.00 3.41
5594 9828 0.603569 AGTCGCCGAAGACAAGTGAT 59.396 50.000 11.68 0.00 43.24 3.06
5638 9872 0.390735 CTAAAAGGTGGGTCCGACGG 60.391 60.000 7.84 7.84 41.99 4.79
5641 9875 1.272807 CTCCTAAAAGGTGGGTCCGA 58.727 55.000 0.00 0.00 41.99 4.55
5655 9889 1.751351 CGACTCAATGACCAGCTCCTA 59.249 52.381 0.00 0.00 0.00 2.94
5676 9910 2.442084 GGACGTCCGTCAATGACAC 58.558 57.895 20.85 4.08 46.20 3.67
5677 9911 4.979204 GGACGTCCGTCAATGACA 57.021 55.556 20.85 0.00 46.20 3.58
5750 9984 1.798813 GTGAAGAACTAGGTGGCGTTG 59.201 52.381 0.00 0.00 0.00 4.10
5752 9986 0.038526 CGTGAAGAACTAGGTGGCGT 60.039 55.000 0.00 0.00 0.00 5.68
5777 10011 3.372730 GGCCAAGGCGTGCATGAA 61.373 61.111 10.93 0.00 43.06 2.57
5778 10012 4.657408 TGGCCAAGGCGTGCATGA 62.657 61.111 10.93 0.00 43.06 3.07
5791 10025 2.027625 CTCGTCCAAAGTCGTGGCC 61.028 63.158 0.00 0.00 38.68 5.36


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

AutoCloner maintained by Alex Coulton.