Multiple sequence alignment - TraesCS3B01G481100

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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 TraesCS3B01G481100 chr3B 100.000 4112 0 0 1 4112 728851297 728855408 0.000000e+00 7594
1 TraesCS3B01G481100 chr3B 97.119 243 6 1 3871 4112 819912532 819912290 3.830000e-110 409
2 TraesCS3B01G481100 chrUn 96.686 3138 103 1 1 3137 134333756 134330619 0.000000e+00 5217
3 TraesCS3B01G481100 chr3D 96.622 3138 105 1 1 3137 579344618 579347755 0.000000e+00 5206
4 TraesCS3B01G481100 chr4D 96.558 3138 107 1 1 3137 502618753 502621890 0.000000e+00 5195
5 TraesCS3B01G481100 chr2D 96.368 3139 112 1 1 3137 82250617 82247479 0.000000e+00 5164
6 TraesCS3B01G481100 chr2D 94.444 162 9 0 3951 4112 37869054 37868893 2.450000e-62 250
7 TraesCS3B01G481100 chr2D 96.774 62 2 0 3871 3932 408526345 408526406 2.020000e-18 104
8 TraesCS3B01G481100 chr6B 95.058 3197 149 6 1 3189 646100958 646104153 0.000000e+00 5020
9 TraesCS3B01G481100 chr6B 98.347 242 4 0 3871 4112 381187695 381187454 3.800000e-115 425
10 TraesCS3B01G481100 chr1A 95.380 2576 116 3 477 3049 394485024 394487599 0.000000e+00 4095
11 TraesCS3B01G481100 chr1A 95.299 2340 108 2 712 3049 394415106 394417445 0.000000e+00 3711
12 TraesCS3B01G481100 chr1A 94.510 255 13 1 3858 4112 551184044 551183791 3.850000e-105 392
13 TraesCS3B01G481100 chr1A 94.628 242 13 0 3871 4112 515557429 515557670 3.880000e-100 375
14 TraesCS3B01G481100 chr1A 94.215 242 14 0 3871 4112 287575226 287575467 1.810000e-98 370
15 TraesCS3B01G481100 chr5A 94.536 2544 135 4 477 3016 542029676 542027133 0.000000e+00 3925
16 TraesCS3B01G481100 chr4B 94.120 2109 115 5 909 3015 524149752 524147651 0.000000e+00 3199
17 TraesCS3B01G481100 chr7D 95.330 1713 78 2 1 1711 109456095 109457807 0.000000e+00 2719
18 TraesCS3B01G481100 chr7D 96.047 430 17 0 2708 3137 109457801 109458230 0.000000e+00 701
19 TraesCS3B01G481100 chr7D 95.161 62 3 0 3871 3932 162157056 162157117 9.410000e-17 99
20 TraesCS3B01G481100 chr4A 94.832 774 35 4 3099 3871 687961129 687960360 0.000000e+00 1203
21 TraesCS3B01G481100 chr5D 97.368 190 5 0 2948 3137 531438778 531438589 1.430000e-84 324
22 TraesCS3B01G481100 chr5D 95.062 162 8 0 3951 4112 501357533 501357372 5.270000e-64 255
23 TraesCS3B01G481100 chr5D 95.161 62 3 0 3871 3932 501358313 501358252 9.410000e-17 99
24 TraesCS3B01G481100 chr1D 95.706 163 6 1 3951 4112 202963547 202963709 1.130000e-65 261
25 TraesCS3B01G481100 chr1D 96.774 62 2 0 3871 3932 202962769 202962830 2.020000e-18 104
26 TraesCS3B01G481100 chr6D 95.062 162 8 0 3951 4112 156818115 156817954 5.270000e-64 255


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 TraesCS3B01G481100 chr3B 728851297 728855408 4111 False 7594 7594 100.0000 1 4112 1 chr3B.!!$F1 4111
1 TraesCS3B01G481100 chrUn 134330619 134333756 3137 True 5217 5217 96.6860 1 3137 1 chrUn.!!$R1 3136
2 TraesCS3B01G481100 chr3D 579344618 579347755 3137 False 5206 5206 96.6220 1 3137 1 chr3D.!!$F1 3136
3 TraesCS3B01G481100 chr4D 502618753 502621890 3137 False 5195 5195 96.5580 1 3137 1 chr4D.!!$F1 3136
4 TraesCS3B01G481100 chr2D 82247479 82250617 3138 True 5164 5164 96.3680 1 3137 1 chr2D.!!$R2 3136
5 TraesCS3B01G481100 chr6B 646100958 646104153 3195 False 5020 5020 95.0580 1 3189 1 chr6B.!!$F1 3188
6 TraesCS3B01G481100 chr1A 394485024 394487599 2575 False 4095 4095 95.3800 477 3049 1 chr1A.!!$F3 2572
7 TraesCS3B01G481100 chr1A 394415106 394417445 2339 False 3711 3711 95.2990 712 3049 1 chr1A.!!$F2 2337
8 TraesCS3B01G481100 chr5A 542027133 542029676 2543 True 3925 3925 94.5360 477 3016 1 chr5A.!!$R1 2539
9 TraesCS3B01G481100 chr4B 524147651 524149752 2101 True 3199 3199 94.1200 909 3015 1 chr4B.!!$R1 2106
10 TraesCS3B01G481100 chr7D 109456095 109458230 2135 False 1710 2719 95.6885 1 3137 2 chr7D.!!$F2 3136
11 TraesCS3B01G481100 chr4A 687960360 687961129 769 True 1203 1203 94.8320 3099 3871 1 chr4A.!!$R1 772

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
193 194 0.689055 AGTCAAGAGCATGCTGGTCA 59.311 50.0 28.27 3.1 46.52 4.02 F
1161 1168 1.304891 CCAACCCCCAGGAGGATTTA 58.695 55.0 0.00 0.0 38.24 1.40 F
2416 2430 0.393132 GTTGCAGGCTAGGGTCCTTC 60.393 60.0 0.00 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 1956 0.511221 GCTCGCAAGCTTACGAACAA 59.489 50.0 21.43 0.85 45.55 2.83 R
2797 2811 0.463833 CAAGGCTGTCGTAATCCCCC 60.464 60.0 0.00 0.00 0.00 5.40 R
3984 4000 0.108138 GCAGCGGTTACTGGTCATCT 60.108 55.0 0.00 0.00 38.16 2.90 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
28 29 4.219944 GTGGGATTCAGTATATAGACGGCA 59.780 45.833 0.00 0.00 0.00 5.69
63 64 8.070034 TGTTGAGATAGGCATCATGAATTTTT 57.930 30.769 0.00 0.00 33.21 1.94
70 71 9.252962 GATAGGCATCATGAATTTTTGGTAAAG 57.747 33.333 0.00 0.00 0.00 1.85
153 154 9.511272 CAACATATCTTTATCATTCCAGATGGA 57.489 33.333 0.00 0.00 43.73 3.41
193 194 0.689055 AGTCAAGAGCATGCTGGTCA 59.311 50.000 28.27 3.10 46.52 4.02
197 198 2.092592 TCAAGAGCATGCTGGTCATCAT 60.093 45.455 28.27 0.00 46.52 2.45
213 214 5.163754 GGTCATCATTTGTACCACTTGTAGC 60.164 44.000 0.00 0.00 32.04 3.58
258 259 5.464965 AATTGCAGTTACGTACATACAGC 57.535 39.130 0.00 0.18 0.00 4.40
302 303 1.606668 GAGACTATGAGGGAGAGCACG 59.393 57.143 0.00 0.00 0.00 5.34
677 679 6.099701 TCAACTCTATGTGTAGCCATTATGGT 59.900 38.462 13.28 2.60 40.46 3.55
714 717 5.603596 TGTACGCATACTTAATTCGGGATT 58.396 37.500 0.00 0.00 32.00 3.01
719 722 5.236478 CGCATACTTAATTCGGGATTTCTGT 59.764 40.000 0.00 0.00 0.00 3.41
802 807 9.474313 TGCCTTAGGAACAAAATATTCAACTAT 57.526 29.630 0.69 0.00 0.00 2.12
879 884 8.752766 AGAATCATCTACGTCTTAAAAACGAA 57.247 30.769 14.85 3.26 42.98 3.85
945 952 7.433680 TCCGTTTATATATATGCTGCATCGAT 58.566 34.615 19.90 15.22 0.00 3.59
1066 1073 2.571757 CGCGCACTTACCAGGAGA 59.428 61.111 8.75 0.00 0.00 3.71
1115 1122 3.015145 CCCCGACCCCAATGAGGT 61.015 66.667 0.00 0.00 41.50 3.85
1132 1139 2.853542 TTGCCCTCCAGCTCCACA 60.854 61.111 0.00 0.00 0.00 4.17
1161 1168 1.304891 CCAACCCCCAGGAGGATTTA 58.695 55.000 0.00 0.00 38.24 1.40
1282 1289 8.138712 AGACACTAGAGTAAGTTATGCTATTGC 58.861 37.037 0.00 0.00 40.20 3.56
1337 1344 2.901338 AGGTCCTACACAGCAGACTA 57.099 50.000 0.00 0.00 0.00 2.59
1612 1620 4.700213 GTGCTACCTAAATTTTCCTGCTCA 59.300 41.667 0.00 0.00 0.00 4.26
1696 1704 5.237127 GCTAGAAGGTGCTGCAAAAATTTTT 59.763 36.000 10.41 10.41 0.00 1.94
1945 1956 1.207089 TCCCGAATGCTTCAATCTCGT 59.793 47.619 0.00 0.00 0.00 4.18
2027 2038 7.440856 GGAGGAAAACATTATTTTGACTTGCAA 59.559 33.333 0.00 0.00 33.88 4.08
2218 2232 6.555315 CAAATAACCTATGTTGACCTTCTGC 58.445 40.000 0.00 0.00 35.87 4.26
2276 2290 6.153170 TCGTATGGTCTACTTGTGGTAAATCA 59.847 38.462 0.00 0.00 0.00 2.57
2416 2430 0.393132 GTTGCAGGCTAGGGTCCTTC 60.393 60.000 0.00 0.00 0.00 3.46
2485 2499 8.599774 CATTCAATTTTCGGCGGTAATTTAATT 58.400 29.630 7.21 0.00 0.00 1.40
2797 2811 1.372087 GCTGCTGGAAACATCCCTCG 61.372 60.000 0.00 0.00 41.51 4.63
2800 2814 1.224592 CTGGAAACATCCCTCGGGG 59.775 63.158 0.00 0.00 41.51 5.73
2810 2824 3.944123 CCTCGGGGGATTACGACA 58.056 61.111 0.00 0.00 37.23 4.35
3185 3200 8.409358 AAAAACAGGCTGAAAATCTACTACAT 57.591 30.769 23.66 0.00 0.00 2.29
3236 3251 1.214367 CGATATTAGGCCGTGCGTTT 58.786 50.000 0.00 0.00 0.00 3.60
3284 3299 6.542005 TGCATCCAATCGTTTACAATGTAGAT 59.458 34.615 0.00 0.00 0.00 1.98
3378 3394 6.907206 AAAAATTTCTGGATTGTGTGTGTG 57.093 33.333 0.00 0.00 0.00 3.82
3381 3397 5.850557 ATTTCTGGATTGTGTGTGTGAAA 57.149 34.783 0.00 0.00 0.00 2.69
3385 3401 7.523293 TTCTGGATTGTGTGTGTGAAAATAT 57.477 32.000 0.00 0.00 0.00 1.28
3386 3402 6.912082 TCTGGATTGTGTGTGTGAAAATATG 58.088 36.000 0.00 0.00 0.00 1.78
3387 3403 6.489700 TCTGGATTGTGTGTGTGAAAATATGT 59.510 34.615 0.00 0.00 0.00 2.29
3496 3512 6.553953 TCATAGTTATTTGCTGTAGGACCA 57.446 37.500 0.00 0.00 0.00 4.02
3508 3524 4.631813 GCTGTAGGACCAATGTGTCTAAAG 59.368 45.833 0.00 0.00 35.54 1.85
3618 3634 6.117488 TCGTTATTCCCCTTATTTTGACCTC 58.883 40.000 0.00 0.00 0.00 3.85
3623 3639 2.290705 CCCCTTATTTTGACCTCCGTGT 60.291 50.000 0.00 0.00 0.00 4.49
3675 3691 9.691362 GGTCTTTTGTTTCTATATTTTGCTTCA 57.309 29.630 0.00 0.00 0.00 3.02
3787 3803 9.590451 AAATTTCTGCCATATTATGAACAGTTG 57.410 29.630 18.36 3.86 36.37 3.16
3814 3830 6.212388 TGTTATGGAAATAAATGTGGCACCTT 59.788 34.615 16.26 8.96 0.00 3.50
3827 3843 1.151450 CACCTTCCAACCTGGTGCT 59.849 57.895 0.00 0.00 43.61 4.40
3834 3850 1.968017 CAACCTGGTGCTGCACGAT 60.968 57.895 24.86 5.90 34.83 3.73
3863 3879 7.618019 TCTGCCCTTAATCTGTACTCAATAT 57.382 36.000 0.00 0.00 0.00 1.28
3865 3881 9.326489 TCTGCCCTTAATCTGTACTCAATATAT 57.674 33.333 0.00 0.00 0.00 0.86
3886 3902 9.983024 ATATATATTCACTAGTAGACTGCCTGT 57.017 33.333 3.59 0.00 0.00 4.00
3887 3903 4.727507 ATTCACTAGTAGACTGCCTGTG 57.272 45.455 3.59 7.04 0.00 3.66
3888 3904 1.819288 TCACTAGTAGACTGCCTGTGC 59.181 52.381 3.59 0.00 38.26 4.57
3889 3905 0.811915 ACTAGTAGACTGCCTGTGCG 59.188 55.000 3.59 0.00 41.78 5.34
3890 3906 0.811915 CTAGTAGACTGCCTGTGCGT 59.188 55.000 0.00 0.00 41.78 5.24
3891 3907 1.202582 CTAGTAGACTGCCTGTGCGTT 59.797 52.381 0.00 0.00 41.78 4.84
3892 3908 0.319900 AGTAGACTGCCTGTGCGTTG 60.320 55.000 0.00 0.00 41.78 4.10
3893 3909 1.667830 TAGACTGCCTGTGCGTTGC 60.668 57.895 0.00 0.00 41.78 4.17
3894 3910 2.376228 TAGACTGCCTGTGCGTTGCA 62.376 55.000 0.00 0.00 41.78 4.08
3895 3911 2.828095 ACTGCCTGTGCGTTGCAA 60.828 55.556 0.00 0.00 41.47 4.08
3896 3912 2.353839 CTGCCTGTGCGTTGCAAC 60.354 61.111 19.89 19.89 41.47 4.17
3907 3923 3.354131 GTTGCAACGGGCTTTTGAA 57.646 47.368 14.90 0.00 45.15 2.69
3908 3924 1.646189 GTTGCAACGGGCTTTTGAAA 58.354 45.000 14.90 0.00 45.15 2.69
3909 3925 2.003301 GTTGCAACGGGCTTTTGAAAA 58.997 42.857 14.90 0.00 45.15 2.29
3910 3926 2.611225 TGCAACGGGCTTTTGAAAAT 57.389 40.000 3.00 0.00 45.15 1.82
3911 3927 2.911484 TGCAACGGGCTTTTGAAAATT 58.089 38.095 3.00 0.00 45.15 1.82
3912 3928 3.274288 TGCAACGGGCTTTTGAAAATTT 58.726 36.364 3.00 0.00 45.15 1.82
3913 3929 3.064545 TGCAACGGGCTTTTGAAAATTTG 59.935 39.130 0.00 0.00 45.15 2.32
3914 3930 3.064682 GCAACGGGCTTTTGAAAATTTGT 59.935 39.130 0.00 0.00 40.25 2.83
3915 3931 4.271291 GCAACGGGCTTTTGAAAATTTGTA 59.729 37.500 0.00 0.00 40.25 2.41
3916 3932 5.049749 GCAACGGGCTTTTGAAAATTTGTAT 60.050 36.000 0.00 0.00 40.25 2.29
3917 3933 6.512578 GCAACGGGCTTTTGAAAATTTGTATT 60.513 34.615 0.00 0.00 40.25 1.89
3918 3934 7.413644 CAACGGGCTTTTGAAAATTTGTATTT 58.586 30.769 0.00 0.00 35.49 1.40
3919 3935 6.953843 ACGGGCTTTTGAAAATTTGTATTTG 58.046 32.000 0.00 0.00 34.27 2.32
3920 3936 6.540551 ACGGGCTTTTGAAAATTTGTATTTGT 59.459 30.769 0.00 0.00 34.27 2.83
3921 3937 7.066404 ACGGGCTTTTGAAAATTTGTATTTGTT 59.934 29.630 0.00 0.00 34.27 2.83
3922 3938 7.375544 CGGGCTTTTGAAAATTTGTATTTGTTG 59.624 33.333 0.00 0.00 34.27 3.33
3923 3939 7.167302 GGGCTTTTGAAAATTTGTATTTGTTGC 59.833 33.333 0.00 0.00 34.27 4.17
3924 3940 7.699812 GGCTTTTGAAAATTTGTATTTGTTGCA 59.300 29.630 0.00 0.00 34.27 4.08
3925 3941 9.235537 GCTTTTGAAAATTTGTATTTGTTGCAT 57.764 25.926 0.00 0.00 34.27 3.96
3928 3944 9.713740 TTTGAAAATTTGTATTTGTTGCATGTC 57.286 25.926 0.00 0.00 34.27 3.06
3929 3945 8.429493 TGAAAATTTGTATTTGTTGCATGTCA 57.571 26.923 0.00 0.00 34.27 3.58
3930 3946 8.886719 TGAAAATTTGTATTTGTTGCATGTCAA 58.113 25.926 0.00 0.00 34.27 3.18
3931 3947 9.713740 GAAAATTTGTATTTGTTGCATGTCAAA 57.286 25.926 12.26 12.26 37.82 2.69
3932 3948 9.500864 AAAATTTGTATTTGTTGCATGTCAAAC 57.499 25.926 12.17 7.67 36.58 2.93
3933 3949 5.879948 TTGTATTTGTTGCATGTCAAACG 57.120 34.783 12.17 0.00 36.58 3.60
3934 3950 5.175090 TGTATTTGTTGCATGTCAAACGA 57.825 34.783 12.17 5.02 36.58 3.85
3935 3951 5.582550 TGTATTTGTTGCATGTCAAACGAA 58.417 33.333 12.17 11.65 36.58 3.85
3936 3952 6.036470 TGTATTTGTTGCATGTCAAACGAAA 58.964 32.000 12.17 8.85 36.58 3.46
3937 3953 5.640218 ATTTGTTGCATGTCAAACGAAAG 57.360 34.783 12.17 0.00 36.58 2.62
3938 3954 4.362932 TTGTTGCATGTCAAACGAAAGA 57.637 36.364 4.47 0.00 36.26 2.52
3939 3955 4.566545 TGTTGCATGTCAAACGAAAGAT 57.433 36.364 4.47 0.00 36.26 2.40
3940 3956 5.681337 TGTTGCATGTCAAACGAAAGATA 57.319 34.783 4.47 0.00 36.26 1.98
3941 3957 6.066054 TGTTGCATGTCAAACGAAAGATAA 57.934 33.333 4.47 0.00 36.26 1.75
3942 3958 6.676950 TGTTGCATGTCAAACGAAAGATAAT 58.323 32.000 4.47 0.00 36.26 1.28
3943 3959 7.811653 TGTTGCATGTCAAACGAAAGATAATA 58.188 30.769 4.47 0.00 36.26 0.98
3944 3960 8.293157 TGTTGCATGTCAAACGAAAGATAATAA 58.707 29.630 4.47 0.00 36.26 1.40
3945 3961 9.289303 GTTGCATGTCAAACGAAAGATAATAAT 57.711 29.630 4.47 0.00 36.26 1.28
3946 3962 9.853555 TTGCATGTCAAACGAAAGATAATAATT 57.146 25.926 0.00 0.00 0.00 1.40
3947 3963 9.288124 TGCATGTCAAACGAAAGATAATAATTG 57.712 29.630 0.00 0.00 0.00 2.32
3948 3964 8.745837 GCATGTCAAACGAAAGATAATAATTGG 58.254 33.333 0.00 0.00 0.00 3.16
3949 3965 8.745837 CATGTCAAACGAAAGATAATAATTGGC 58.254 33.333 0.00 0.00 0.00 4.52
3950 3966 7.821652 TGTCAAACGAAAGATAATAATTGGCA 58.178 30.769 0.00 0.00 0.00 4.92
3951 3967 8.300286 TGTCAAACGAAAGATAATAATTGGCAA 58.700 29.630 0.68 0.68 29.27 4.52
3952 3968 8.583765 GTCAAACGAAAGATAATAATTGGCAAC 58.416 33.333 0.00 0.00 0.00 4.17
3967 3983 3.477504 CAACAAATGCCGACACTGG 57.522 52.632 0.00 0.00 0.00 4.00
3968 3984 0.667993 CAACAAATGCCGACACTGGT 59.332 50.000 0.00 0.00 0.00 4.00
3969 3985 1.876799 CAACAAATGCCGACACTGGTA 59.123 47.619 0.00 0.00 0.00 3.25
3970 3986 1.808411 ACAAATGCCGACACTGGTAG 58.192 50.000 0.00 0.00 0.00 3.18
3971 3987 1.346395 ACAAATGCCGACACTGGTAGA 59.654 47.619 0.00 0.00 0.00 2.59
3972 3988 2.027192 ACAAATGCCGACACTGGTAGAT 60.027 45.455 0.00 0.00 0.00 1.98
3973 3989 2.604046 AATGCCGACACTGGTAGATC 57.396 50.000 0.00 0.00 0.00 2.75
3974 3990 1.485124 ATGCCGACACTGGTAGATCA 58.515 50.000 0.00 0.00 0.00 2.92
3975 3991 1.262417 TGCCGACACTGGTAGATCAA 58.738 50.000 0.00 0.00 0.00 2.57
3976 3992 1.067142 TGCCGACACTGGTAGATCAAC 60.067 52.381 0.00 0.00 0.00 3.18
3977 3993 1.909376 CCGACACTGGTAGATCAACG 58.091 55.000 0.00 0.00 0.00 4.10
3978 3994 1.471287 CCGACACTGGTAGATCAACGA 59.529 52.381 0.00 0.00 0.00 3.85
3979 3995 2.094906 CCGACACTGGTAGATCAACGAA 60.095 50.000 0.00 0.00 0.00 3.85
3980 3996 3.571571 CGACACTGGTAGATCAACGAAA 58.428 45.455 0.00 0.00 0.00 3.46
3981 3997 3.364023 CGACACTGGTAGATCAACGAAAC 59.636 47.826 0.00 0.00 0.00 2.78
3982 3998 4.304110 GACACTGGTAGATCAACGAAACA 58.696 43.478 0.00 0.00 0.00 2.83
3983 3999 4.699637 ACACTGGTAGATCAACGAAACAA 58.300 39.130 0.00 0.00 0.00 2.83
3984 4000 5.120399 ACACTGGTAGATCAACGAAACAAA 58.880 37.500 0.00 0.00 0.00 2.83
3985 4001 5.236478 ACACTGGTAGATCAACGAAACAAAG 59.764 40.000 0.00 0.00 0.00 2.77
3986 4002 5.465390 CACTGGTAGATCAACGAAACAAAGA 59.535 40.000 0.00 0.00 0.00 2.52
3987 4003 6.147821 CACTGGTAGATCAACGAAACAAAGAT 59.852 38.462 0.00 0.00 0.00 2.40
3988 4004 6.147821 ACTGGTAGATCAACGAAACAAAGATG 59.852 38.462 0.00 0.00 0.00 2.90
3989 4005 6.227522 TGGTAGATCAACGAAACAAAGATGA 58.772 36.000 0.00 0.00 0.00 2.92
3990 4006 6.147164 TGGTAGATCAACGAAACAAAGATGAC 59.853 38.462 0.00 0.00 0.00 3.06
3991 4007 5.613358 AGATCAACGAAACAAAGATGACC 57.387 39.130 0.00 0.00 0.00 4.02
3992 4008 5.063204 AGATCAACGAAACAAAGATGACCA 58.937 37.500 0.00 0.00 0.00 4.02
3993 4009 4.811555 TCAACGAAACAAAGATGACCAG 57.188 40.909 0.00 0.00 0.00 4.00
3994 4010 4.196193 TCAACGAAACAAAGATGACCAGT 58.804 39.130 0.00 0.00 0.00 4.00
3995 4011 5.361427 TCAACGAAACAAAGATGACCAGTA 58.639 37.500 0.00 0.00 0.00 2.74
3996 4012 5.818336 TCAACGAAACAAAGATGACCAGTAA 59.182 36.000 0.00 0.00 0.00 2.24
3997 4013 5.668558 ACGAAACAAAGATGACCAGTAAC 57.331 39.130 0.00 0.00 0.00 2.50
3998 4014 4.514066 ACGAAACAAAGATGACCAGTAACC 59.486 41.667 0.00 0.00 0.00 2.85
3999 4015 4.377022 CGAAACAAAGATGACCAGTAACCG 60.377 45.833 0.00 0.00 0.00 4.44
4000 4016 2.423577 ACAAAGATGACCAGTAACCGC 58.576 47.619 0.00 0.00 0.00 5.68
4001 4017 2.038557 ACAAAGATGACCAGTAACCGCT 59.961 45.455 0.00 0.00 0.00 5.52
4002 4018 2.386661 AAGATGACCAGTAACCGCTG 57.613 50.000 0.00 0.00 36.31 5.18
4003 4019 0.108138 AGATGACCAGTAACCGCTGC 60.108 55.000 0.00 0.00 35.28 5.25
4004 4020 0.391130 GATGACCAGTAACCGCTGCA 60.391 55.000 0.00 0.00 35.28 4.41
4005 4021 0.673644 ATGACCAGTAACCGCTGCAC 60.674 55.000 0.00 0.00 35.28 4.57
4006 4022 2.032071 ACCAGTAACCGCTGCACC 59.968 61.111 0.00 0.00 35.28 5.01
4007 4023 3.118454 CCAGTAACCGCTGCACCG 61.118 66.667 0.00 0.00 35.28 4.94
4008 4024 2.357034 CAGTAACCGCTGCACCGT 60.357 61.111 0.00 0.00 0.00 4.83
4009 4025 2.048503 AGTAACCGCTGCACCGTC 60.049 61.111 0.00 0.00 0.00 4.79
4010 4026 3.116531 GTAACCGCTGCACCGTCC 61.117 66.667 0.00 0.00 0.00 4.79
4011 4027 4.728102 TAACCGCTGCACCGTCCG 62.728 66.667 0.00 0.00 0.00 4.79
4030 4046 4.806571 TGAAGTATCACCGCGCTC 57.193 55.556 5.56 0.00 0.00 5.03
4031 4047 1.141019 TGAAGTATCACCGCGCTCC 59.859 57.895 5.56 0.00 0.00 4.70
4032 4048 1.320344 TGAAGTATCACCGCGCTCCT 61.320 55.000 5.56 0.00 0.00 3.69
4033 4049 0.666913 GAAGTATCACCGCGCTCCTA 59.333 55.000 5.56 0.00 0.00 2.94
4034 4050 0.669077 AAGTATCACCGCGCTCCTAG 59.331 55.000 5.56 0.00 0.00 3.02
4035 4051 1.371881 GTATCACCGCGCTCCTAGC 60.372 63.158 5.56 0.00 38.02 3.42
4036 4052 1.826487 TATCACCGCGCTCCTAGCA 60.826 57.895 5.56 0.00 42.58 3.49
4037 4053 2.071844 TATCACCGCGCTCCTAGCAC 62.072 60.000 5.56 0.00 42.58 4.40
4042 4058 4.143333 GCGCTCCTAGCACCCGAA 62.143 66.667 0.00 0.00 42.58 4.30
4043 4059 2.105128 CGCTCCTAGCACCCGAAG 59.895 66.667 0.00 0.00 42.58 3.79
4044 4060 2.202946 GCTCCTAGCACCCGAAGC 60.203 66.667 0.00 0.00 41.89 3.86
4045 4061 2.105128 CTCCTAGCACCCGAAGCG 59.895 66.667 0.00 0.00 37.01 4.68
4046 4062 2.678934 TCCTAGCACCCGAAGCGT 60.679 61.111 0.00 0.00 37.01 5.07
4047 4063 2.202756 CCTAGCACCCGAAGCGTC 60.203 66.667 0.00 0.00 37.01 5.19
4049 4065 4.789075 TAGCACCCGAAGCGTCGC 62.789 66.667 16.96 9.80 46.28 5.19
4052 4068 2.202690 CACCCGAAGCGTCGCATA 60.203 61.111 21.09 0.00 46.28 3.14
4053 4069 2.202703 ACCCGAAGCGTCGCATAC 60.203 61.111 21.09 8.97 46.28 2.39
4054 4070 2.202690 CCCGAAGCGTCGCATACA 60.203 61.111 21.09 0.00 46.28 2.29
4055 4071 2.230940 CCCGAAGCGTCGCATACAG 61.231 63.158 21.09 5.66 46.28 2.74
4056 4072 1.226575 CCGAAGCGTCGCATACAGA 60.227 57.895 21.09 0.00 46.28 3.41
4057 4073 1.202973 CCGAAGCGTCGCATACAGAG 61.203 60.000 21.09 3.15 46.28 3.35
4058 4074 1.802300 CGAAGCGTCGCATACAGAGC 61.802 60.000 21.09 0.00 41.08 4.09
4059 4075 0.802222 GAAGCGTCGCATACAGAGCA 60.802 55.000 21.09 0.00 0.00 4.26
4060 4076 0.389817 AAGCGTCGCATACAGAGCAA 60.390 50.000 21.09 0.00 0.00 3.91
4061 4077 1.078759 AGCGTCGCATACAGAGCAAC 61.079 55.000 21.09 0.00 0.00 4.17
4062 4078 1.351430 GCGTCGCATACAGAGCAACA 61.351 55.000 13.44 0.00 0.00 3.33
4063 4079 0.366871 CGTCGCATACAGAGCAACAC 59.633 55.000 0.00 0.00 0.00 3.32
4064 4080 0.721718 GTCGCATACAGAGCAACACC 59.278 55.000 0.00 0.00 0.00 4.16
4065 4081 0.608130 TCGCATACAGAGCAACACCT 59.392 50.000 0.00 0.00 0.00 4.00
4066 4082 1.001974 TCGCATACAGAGCAACACCTT 59.998 47.619 0.00 0.00 0.00 3.50
4067 4083 1.394917 CGCATACAGAGCAACACCTTC 59.605 52.381 0.00 0.00 0.00 3.46
4068 4084 2.426522 GCATACAGAGCAACACCTTCA 58.573 47.619 0.00 0.00 0.00 3.02
4069 4085 2.813754 GCATACAGAGCAACACCTTCAA 59.186 45.455 0.00 0.00 0.00 2.69
4070 4086 3.120060 GCATACAGAGCAACACCTTCAAG 60.120 47.826 0.00 0.00 0.00 3.02
4071 4087 4.318332 CATACAGAGCAACACCTTCAAGA 58.682 43.478 0.00 0.00 0.00 3.02
4072 4088 3.281727 ACAGAGCAACACCTTCAAGAA 57.718 42.857 0.00 0.00 0.00 2.52
4073 4089 3.209410 ACAGAGCAACACCTTCAAGAAG 58.791 45.455 2.83 2.83 38.14 2.85
4083 4099 2.795121 CTTCAAGAAGGAATGCGACG 57.205 50.000 1.86 0.00 34.87 5.12
4084 4100 2.337583 CTTCAAGAAGGAATGCGACGA 58.662 47.619 0.00 0.00 34.87 4.20
4085 4101 1.710013 TCAAGAAGGAATGCGACGAC 58.290 50.000 0.00 0.00 0.00 4.34
4086 4102 0.366871 CAAGAAGGAATGCGACGACG 59.633 55.000 2.12 2.12 42.93 5.12
4087 4103 0.242825 AAGAAGGAATGCGACGACGA 59.757 50.000 12.29 0.00 42.66 4.20
4088 4104 0.456312 AGAAGGAATGCGACGACGAC 60.456 55.000 12.29 3.11 42.66 4.34
4089 4105 1.730593 GAAGGAATGCGACGACGACG 61.731 60.000 15.13 15.13 42.66 5.12
4097 4113 4.702081 GACGACGACGCCACTGCT 62.702 66.667 7.30 0.00 43.96 4.24
4107 4123 4.641645 CCACTGCTGCCCGGACAA 62.642 66.667 0.73 0.00 0.00 3.18
4108 4124 3.052082 CACTGCTGCCCGGACAAG 61.052 66.667 0.73 0.00 0.00 3.16
4109 4125 3.560251 ACTGCTGCCCGGACAAGT 61.560 61.111 0.73 0.00 0.00 3.16
4110 4126 2.743928 CTGCTGCCCGGACAAGTC 60.744 66.667 0.73 0.00 0.00 3.01
4111 4127 4.329545 TGCTGCCCGGACAAGTCC 62.330 66.667 0.73 9.22 46.18 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.263905 TGCCTATCTCAACAAAATGGACCT 60.264 41.667 0.00 0.00 0.00 3.85
63 64 6.428083 TCAAGTACTGATTGGACTTTACCA 57.572 37.500 0.00 0.00 38.24 3.25
70 71 7.923414 ATAAAACCTCAAGTACTGATTGGAC 57.077 36.000 0.00 0.00 32.14 4.02
150 151 8.480501 ACTTAGGCGTATAAAAAGTATCTTCCA 58.519 33.333 0.00 0.00 0.00 3.53
153 154 9.880157 TTGACTTAGGCGTATAAAAAGTATCTT 57.120 29.630 0.00 0.00 30.83 2.40
193 194 3.374058 GCGCTACAAGTGGTACAAATGAT 59.626 43.478 0.00 0.00 44.16 2.45
197 198 1.868498 GTGCGCTACAAGTGGTACAAA 59.132 47.619 9.73 0.00 44.16 2.83
213 214 6.726035 TTTCTCGAACAAATTTTTAGTGCG 57.274 33.333 1.94 1.94 35.66 5.34
258 259 4.487714 TGCACTTATCCCTCTGGTTTAG 57.512 45.455 0.00 0.00 0.00 1.85
302 303 0.395312 TGTCGGGGGAGAACAAGAAC 59.605 55.000 0.00 0.00 0.00 3.01
443 445 3.691118 GTGTCATTAAGCAGGCTTCATGA 59.309 43.478 20.96 20.96 41.52 3.07
446 448 3.423539 AGTGTCATTAAGCAGGCTTCA 57.576 42.857 10.21 0.00 37.47 3.02
636 638 9.252962 CATAGAGTTGACAAGCAAAAAGAAAAT 57.747 29.630 0.00 0.00 38.44 1.82
661 663 6.740944 ACATACTACCATAATGGCTACACA 57.259 37.500 0.00 0.00 42.67 3.72
802 807 6.761714 GGCGTATCAGATCTTTCTCCTTTTTA 59.238 38.462 0.00 0.00 0.00 1.52
945 952 4.473196 TGAGGTGTCTTGGCAATTAGGATA 59.527 41.667 0.00 0.00 0.00 2.59
1027 1034 2.264480 CACAACCTGGATCGCCGA 59.736 61.111 0.00 0.00 36.79 5.54
1115 1122 1.792757 ATTGTGGAGCTGGAGGGCAA 61.793 55.000 0.00 0.00 34.17 4.52
1132 1139 2.604382 GGGGTTGGCCACAGCATT 60.604 61.111 3.88 0.00 42.56 3.56
1144 1151 1.305886 GGTAAATCCTCCTGGGGGTT 58.694 55.000 13.53 0.17 35.33 4.11
1161 1168 2.142292 GAAGATGCAGGGGTGTGGGT 62.142 60.000 0.00 0.00 0.00 4.51
1200 1207 4.679373 ATATTCGAGTGCATCTTCCACT 57.321 40.909 0.00 0.00 45.61 4.00
1302 1309 9.352191 GTGTAGGACCTAGTTCTAATGAGATTA 57.648 37.037 0.00 0.00 0.00 1.75
1323 1330 9.404348 CTATATCAAACATAGTCTGCTGTGTAG 57.596 37.037 0.00 0.00 44.56 2.74
1945 1956 0.511221 GCTCGCAAGCTTACGAACAA 59.489 50.000 21.43 0.85 45.55 2.83
2197 2211 5.045578 ACTGCAGAAGGTCAACATAGGTTAT 60.046 40.000 23.35 0.00 34.87 1.89
2276 2290 8.517323 AAATATGATAACCCTTCTCCTCATCT 57.483 34.615 0.00 0.00 0.00 2.90
2416 2430 1.660607 CATGAGTTCGGTGTTCCATCG 59.339 52.381 0.00 0.00 39.56 3.84
2739 2753 2.906389 TGAGCATCTGGACTACCACTTT 59.094 45.455 0.00 0.00 41.77 2.66
2797 2811 0.463833 CAAGGCTGTCGTAATCCCCC 60.464 60.000 0.00 0.00 0.00 5.40
2800 2814 1.473434 CCCTCAAGGCTGTCGTAATCC 60.473 57.143 0.00 0.00 0.00 3.01
2808 2822 2.031870 GTTCAAAACCCTCAAGGCTGT 58.968 47.619 0.00 0.00 40.58 4.40
2810 2824 2.430694 GTTGTTCAAAACCCTCAAGGCT 59.569 45.455 0.00 0.00 40.58 4.58
3077 3092 7.981789 TCTTGAGTCGCTAAACATATCAGAAAT 59.018 33.333 0.00 0.00 0.00 2.17
3185 3200 9.936759 TTGTGGATGCTGTTCGATTTATATATA 57.063 29.630 0.00 0.00 0.00 0.86
3368 3384 6.971756 CACAGAACATATTTTCACACACACAA 59.028 34.615 4.50 0.00 0.00 3.33
3377 3393 5.301555 TCGACCACACAGAACATATTTTCA 58.698 37.500 4.50 0.00 0.00 2.69
3378 3394 5.856126 TCGACCACACAGAACATATTTTC 57.144 39.130 0.00 0.00 0.00 2.29
3381 3397 5.084818 TGATCGACCACACAGAACATATT 57.915 39.130 0.00 0.00 0.00 1.28
3385 3401 2.869801 GTTTGATCGACCACACAGAACA 59.130 45.455 0.00 0.00 0.00 3.18
3386 3402 2.869801 TGTTTGATCGACCACACAGAAC 59.130 45.455 0.00 0.00 0.00 3.01
3387 3403 3.186702 TGTTTGATCGACCACACAGAA 57.813 42.857 0.00 0.00 0.00 3.02
3478 3494 5.183140 ACACATTGGTCCTACAGCAAATAAC 59.817 40.000 0.00 0.00 45.53 1.89
3496 3512 5.710984 CGAGGACACTACTTTAGACACATT 58.289 41.667 0.00 0.00 0.00 2.71
3508 3524 2.531206 GTTCATCTGCGAGGACACTAC 58.469 52.381 0.00 0.00 0.00 2.73
3784 3800 7.386299 TGCCACATTTATTTCCATAACAACAAC 59.614 33.333 0.00 0.00 0.00 3.32
3787 3803 6.312672 GGTGCCACATTTATTTCCATAACAAC 59.687 38.462 0.00 0.00 0.00 3.32
3814 3830 2.203337 GTGCAGCACCAGGTTGGA 60.203 61.111 15.27 0.00 40.96 3.53
3827 3843 1.451927 GGGCAGATCCAATCGTGCA 60.452 57.895 4.94 0.00 36.10 4.57
3834 3850 4.721776 AGTACAGATTAAGGGCAGATCCAA 59.278 41.667 0.00 0.00 36.21 3.53
3863 3879 6.016192 GCACAGGCAGTCTACTAGTGAATATA 60.016 42.308 5.39 0.00 40.72 0.86
3865 3881 4.098044 GCACAGGCAGTCTACTAGTGAATA 59.902 45.833 5.39 0.00 40.72 1.75
3871 3887 0.811915 ACGCACAGGCAGTCTACTAG 59.188 55.000 0.00 0.00 41.24 2.57
3872 3888 1.067846 CAACGCACAGGCAGTCTACTA 60.068 52.381 0.00 0.00 41.24 1.82
3873 3889 0.319900 CAACGCACAGGCAGTCTACT 60.320 55.000 0.00 0.00 41.24 2.57
3874 3890 1.901650 GCAACGCACAGGCAGTCTAC 61.902 60.000 0.00 0.00 41.24 2.59
3875 3891 1.667830 GCAACGCACAGGCAGTCTA 60.668 57.895 0.00 0.00 41.24 2.59
3876 3892 2.974698 GCAACGCACAGGCAGTCT 60.975 61.111 0.00 0.00 41.24 3.24
3877 3893 2.833533 TTGCAACGCACAGGCAGTC 61.834 57.895 0.00 0.00 38.71 3.51
3878 3894 2.828095 TTGCAACGCACAGGCAGT 60.828 55.556 0.00 0.00 38.71 4.40
3879 3895 2.353839 GTTGCAACGCACAGGCAG 60.354 61.111 14.90 0.00 38.71 4.85
3880 3896 4.249020 CGTTGCAACGCACAGGCA 62.249 61.111 35.89 0.00 46.06 4.75
3889 3905 1.646189 TTTCAAAAGCCCGTTGCAAC 58.354 45.000 19.89 19.89 44.83 4.17
3890 3906 2.386661 TTTTCAAAAGCCCGTTGCAA 57.613 40.000 0.00 0.00 44.83 4.08
3891 3907 2.611225 ATTTTCAAAAGCCCGTTGCA 57.389 40.000 0.00 0.00 44.83 4.08
3892 3908 3.064682 ACAAATTTTCAAAAGCCCGTTGC 59.935 39.130 0.00 0.00 41.71 4.17
3893 3909 4.873768 ACAAATTTTCAAAAGCCCGTTG 57.126 36.364 0.00 0.00 0.00 4.10
3894 3910 7.066404 ACAAATACAAATTTTCAAAAGCCCGTT 59.934 29.630 0.00 0.00 32.87 4.44
3895 3911 6.540551 ACAAATACAAATTTTCAAAAGCCCGT 59.459 30.769 0.00 0.00 32.87 5.28
3896 3912 6.953843 ACAAATACAAATTTTCAAAAGCCCG 58.046 32.000 0.00 0.00 32.87 6.13
3897 3913 7.167302 GCAACAAATACAAATTTTCAAAAGCCC 59.833 33.333 0.00 0.00 32.87 5.19
3898 3914 7.699812 TGCAACAAATACAAATTTTCAAAAGCC 59.300 29.630 0.00 0.00 32.87 4.35
3899 3915 8.612233 TGCAACAAATACAAATTTTCAAAAGC 57.388 26.923 0.00 0.00 32.87 3.51
3902 3918 9.713740 GACATGCAACAAATACAAATTTTCAAA 57.286 25.926 0.00 0.00 32.87 2.69
3903 3919 8.886719 TGACATGCAACAAATACAAATTTTCAA 58.113 25.926 0.00 0.00 32.87 2.69
3904 3920 8.429493 TGACATGCAACAAATACAAATTTTCA 57.571 26.923 0.00 0.00 32.87 2.69
3905 3921 9.713740 TTTGACATGCAACAAATACAAATTTTC 57.286 25.926 11.21 0.00 35.91 2.29
3906 3922 9.500864 GTTTGACATGCAACAAATACAAATTTT 57.499 25.926 15.99 0.00 38.09 1.82
3907 3923 7.850003 CGTTTGACATGCAACAAATACAAATTT 59.150 29.630 15.99 0.00 38.09 1.82
3908 3924 7.223582 TCGTTTGACATGCAACAAATACAAATT 59.776 29.630 15.99 0.00 38.09 1.82
3909 3925 6.699204 TCGTTTGACATGCAACAAATACAAAT 59.301 30.769 15.99 0.00 38.09 2.32
3910 3926 6.036470 TCGTTTGACATGCAACAAATACAAA 58.964 32.000 15.99 8.54 38.09 2.83
3911 3927 5.582550 TCGTTTGACATGCAACAAATACAA 58.417 33.333 15.99 3.97 38.09 2.41
3912 3928 5.175090 TCGTTTGACATGCAACAAATACA 57.825 34.783 15.99 5.28 38.09 2.29
3913 3929 6.416455 TCTTTCGTTTGACATGCAACAAATAC 59.584 34.615 15.99 7.80 38.09 1.89
3914 3930 6.499172 TCTTTCGTTTGACATGCAACAAATA 58.501 32.000 15.99 8.37 38.09 1.40
3915 3931 5.347342 TCTTTCGTTTGACATGCAACAAAT 58.653 33.333 15.99 0.00 38.09 2.32
3916 3932 4.738124 TCTTTCGTTTGACATGCAACAAA 58.262 34.783 11.21 11.21 35.91 2.83
3917 3933 4.362932 TCTTTCGTTTGACATGCAACAA 57.637 36.364 0.00 0.00 35.91 2.83
3918 3934 4.566545 ATCTTTCGTTTGACATGCAACA 57.433 36.364 0.00 0.00 35.91 3.33
3919 3935 8.667987 TTATTATCTTTCGTTTGACATGCAAC 57.332 30.769 0.00 0.00 35.91 4.17
3920 3936 9.853555 AATTATTATCTTTCGTTTGACATGCAA 57.146 25.926 0.00 0.00 33.88 4.08
3921 3937 9.288124 CAATTATTATCTTTCGTTTGACATGCA 57.712 29.630 0.00 0.00 0.00 3.96
3922 3938 8.745837 CCAATTATTATCTTTCGTTTGACATGC 58.254 33.333 0.00 0.00 0.00 4.06
3923 3939 8.745837 GCCAATTATTATCTTTCGTTTGACATG 58.254 33.333 0.00 0.00 0.00 3.21
3924 3940 8.465999 TGCCAATTATTATCTTTCGTTTGACAT 58.534 29.630 0.00 0.00 0.00 3.06
3925 3941 7.821652 TGCCAATTATTATCTTTCGTTTGACA 58.178 30.769 0.00 0.00 0.00 3.58
3926 3942 8.583765 GTTGCCAATTATTATCTTTCGTTTGAC 58.416 33.333 0.00 0.00 0.00 3.18
3927 3943 8.300286 TGTTGCCAATTATTATCTTTCGTTTGA 58.700 29.630 0.00 0.00 0.00 2.69
3928 3944 8.459521 TGTTGCCAATTATTATCTTTCGTTTG 57.540 30.769 0.00 0.00 0.00 2.93
3929 3945 9.482627 TTTGTTGCCAATTATTATCTTTCGTTT 57.517 25.926 0.00 0.00 0.00 3.60
3930 3946 9.651913 ATTTGTTGCCAATTATTATCTTTCGTT 57.348 25.926 0.00 0.00 0.00 3.85
3931 3947 9.086336 CATTTGTTGCCAATTATTATCTTTCGT 57.914 29.630 0.00 0.00 0.00 3.85
3932 3948 8.057742 GCATTTGTTGCCAATTATTATCTTTCG 58.942 33.333 0.00 0.00 46.15 3.46
3949 3965 0.667993 ACCAGTGTCGGCATTTGTTG 59.332 50.000 0.00 0.00 0.00 3.33
3950 3966 2.151202 CTACCAGTGTCGGCATTTGTT 58.849 47.619 0.00 0.00 0.00 2.83
3951 3967 1.346395 TCTACCAGTGTCGGCATTTGT 59.654 47.619 0.00 0.00 0.00 2.83
3952 3968 2.093306 TCTACCAGTGTCGGCATTTG 57.907 50.000 0.00 0.00 0.00 2.32
3953 3969 2.236146 TGATCTACCAGTGTCGGCATTT 59.764 45.455 0.00 0.00 0.00 2.32
3954 3970 1.831106 TGATCTACCAGTGTCGGCATT 59.169 47.619 0.00 0.00 0.00 3.56
3955 3971 1.485124 TGATCTACCAGTGTCGGCAT 58.515 50.000 0.00 0.00 0.00 4.40
3956 3972 1.067142 GTTGATCTACCAGTGTCGGCA 60.067 52.381 0.00 0.00 0.00 5.69
3957 3973 1.641577 GTTGATCTACCAGTGTCGGC 58.358 55.000 0.00 0.00 0.00 5.54
3958 3974 1.471287 TCGTTGATCTACCAGTGTCGG 59.529 52.381 1.57 0.00 0.00 4.79
3959 3975 2.913777 TCGTTGATCTACCAGTGTCG 57.086 50.000 1.57 0.00 0.00 4.35
3960 3976 4.304110 TGTTTCGTTGATCTACCAGTGTC 58.696 43.478 1.57 0.00 0.00 3.67
3961 3977 4.330944 TGTTTCGTTGATCTACCAGTGT 57.669 40.909 1.57 0.00 0.00 3.55
3962 3978 5.465390 TCTTTGTTTCGTTGATCTACCAGTG 59.535 40.000 1.57 0.00 0.00 3.66
3963 3979 5.607477 TCTTTGTTTCGTTGATCTACCAGT 58.393 37.500 1.57 0.00 0.00 4.00
3964 3980 6.368791 TCATCTTTGTTTCGTTGATCTACCAG 59.631 38.462 1.57 0.00 0.00 4.00
3965 3981 6.147164 GTCATCTTTGTTTCGTTGATCTACCA 59.853 38.462 1.57 0.00 0.00 3.25
3966 3982 6.402226 GGTCATCTTTGTTTCGTTGATCTACC 60.402 42.308 1.57 0.00 0.00 3.18
3967 3983 6.147164 TGGTCATCTTTGTTTCGTTGATCTAC 59.853 38.462 0.00 0.00 0.00 2.59
3968 3984 6.227522 TGGTCATCTTTGTTTCGTTGATCTA 58.772 36.000 0.00 0.00 0.00 1.98
3969 3985 5.063204 TGGTCATCTTTGTTTCGTTGATCT 58.937 37.500 0.00 0.00 0.00 2.75
3970 3986 5.049405 ACTGGTCATCTTTGTTTCGTTGATC 60.049 40.000 0.00 0.00 0.00 2.92
3971 3987 4.821805 ACTGGTCATCTTTGTTTCGTTGAT 59.178 37.500 0.00 0.00 0.00 2.57
3972 3988 4.196193 ACTGGTCATCTTTGTTTCGTTGA 58.804 39.130 0.00 0.00 0.00 3.18
3973 3989 4.552166 ACTGGTCATCTTTGTTTCGTTG 57.448 40.909 0.00 0.00 0.00 4.10
3974 3990 5.008316 GGTTACTGGTCATCTTTGTTTCGTT 59.992 40.000 0.00 0.00 0.00 3.85
3975 3991 4.514066 GGTTACTGGTCATCTTTGTTTCGT 59.486 41.667 0.00 0.00 0.00 3.85
3976 3992 4.377022 CGGTTACTGGTCATCTTTGTTTCG 60.377 45.833 0.00 0.00 0.00 3.46
3977 3993 4.612939 GCGGTTACTGGTCATCTTTGTTTC 60.613 45.833 0.00 0.00 0.00 2.78
3978 3994 3.252458 GCGGTTACTGGTCATCTTTGTTT 59.748 43.478 0.00 0.00 0.00 2.83
3979 3995 2.812011 GCGGTTACTGGTCATCTTTGTT 59.188 45.455 0.00 0.00 0.00 2.83
3980 3996 2.038557 AGCGGTTACTGGTCATCTTTGT 59.961 45.455 0.00 0.00 0.00 2.83
3981 3997 2.416547 CAGCGGTTACTGGTCATCTTTG 59.583 50.000 0.00 0.00 33.85 2.77
3982 3998 2.699954 CAGCGGTTACTGGTCATCTTT 58.300 47.619 0.00 0.00 33.85 2.52
3983 3999 1.676014 GCAGCGGTTACTGGTCATCTT 60.676 52.381 0.00 0.00 38.16 2.40
3984 4000 0.108138 GCAGCGGTTACTGGTCATCT 60.108 55.000 0.00 0.00 38.16 2.90
3985 4001 0.391130 TGCAGCGGTTACTGGTCATC 60.391 55.000 0.00 0.00 38.16 2.92
3986 4002 0.673644 GTGCAGCGGTTACTGGTCAT 60.674 55.000 0.00 0.00 38.16 3.06
3987 4003 1.301401 GTGCAGCGGTTACTGGTCA 60.301 57.895 0.00 0.00 38.16 4.02
3988 4004 2.033194 GGTGCAGCGGTTACTGGTC 61.033 63.158 0.00 0.00 38.16 4.02
3989 4005 2.032071 GGTGCAGCGGTTACTGGT 59.968 61.111 0.00 0.00 38.16 4.00
3990 4006 3.118454 CGGTGCAGCGGTTACTGG 61.118 66.667 29.65 0.00 38.16 4.00
3991 4007 2.357034 ACGGTGCAGCGGTTACTG 60.357 61.111 37.73 12.80 40.80 2.74
3992 4008 2.048503 GACGGTGCAGCGGTTACT 60.049 61.111 37.73 19.94 0.00 2.24
3993 4009 3.116531 GGACGGTGCAGCGGTTAC 61.117 66.667 37.73 25.04 0.00 2.50
3994 4010 4.728102 CGGACGGTGCAGCGGTTA 62.728 66.667 37.73 0.00 0.00 2.85
4005 4021 3.340727 GTGATACTTCACCGGACGG 57.659 57.895 9.46 9.56 45.45 4.79
4013 4029 1.141019 GGAGCGCGGTGATACTTCA 59.859 57.895 18.92 0.00 0.00 3.02
4014 4030 0.666913 TAGGAGCGCGGTGATACTTC 59.333 55.000 18.92 0.00 0.00 3.01
4015 4031 0.669077 CTAGGAGCGCGGTGATACTT 59.331 55.000 18.92 0.00 0.00 2.24
4016 4032 1.797211 GCTAGGAGCGCGGTGATACT 61.797 60.000 18.92 11.05 0.00 2.12
4017 4033 1.371881 GCTAGGAGCGCGGTGATAC 60.372 63.158 18.92 0.00 0.00 2.24
4018 4034 1.826487 TGCTAGGAGCGCGGTGATA 60.826 57.895 18.92 7.26 46.26 2.15
4019 4035 3.147595 TGCTAGGAGCGCGGTGAT 61.148 61.111 18.92 6.27 46.26 3.06
4020 4036 4.129737 GTGCTAGGAGCGCGGTGA 62.130 66.667 18.92 0.00 46.26 4.02
4026 4042 2.105128 CTTCGGGTGCTAGGAGCG 59.895 66.667 7.39 3.45 46.26 5.03
4027 4043 2.202946 GCTTCGGGTGCTAGGAGC 60.203 66.667 4.65 4.65 42.82 4.70
4028 4044 2.105128 CGCTTCGGGTGCTAGGAG 59.895 66.667 0.00 0.00 0.00 3.69
4029 4045 2.678934 ACGCTTCGGGTGCTAGGA 60.679 61.111 0.00 0.00 0.00 2.94
4030 4046 2.202756 GACGCTTCGGGTGCTAGG 60.203 66.667 0.00 0.00 0.00 3.02
4031 4047 2.579787 CGACGCTTCGGGTGCTAG 60.580 66.667 4.41 0.00 41.89 3.42
4032 4048 4.789075 GCGACGCTTCGGGTGCTA 62.789 66.667 13.73 0.00 45.98 3.49
4035 4051 2.202690 TATGCGACGCTTCGGGTG 60.203 61.111 22.08 0.00 45.98 4.61
4036 4052 2.202703 GTATGCGACGCTTCGGGT 60.203 61.111 22.08 2.85 45.98 5.28
4037 4053 2.202690 TGTATGCGACGCTTCGGG 60.203 61.111 22.08 0.00 45.98 5.14
4038 4054 1.202973 CTCTGTATGCGACGCTTCGG 61.203 60.000 22.08 15.08 45.98 4.30
4040 4056 0.802222 TGCTCTGTATGCGACGCTTC 60.802 55.000 22.08 11.41 0.00 3.86
4041 4057 0.389817 TTGCTCTGTATGCGACGCTT 60.390 50.000 22.08 17.38 0.00 4.68
4042 4058 1.078759 GTTGCTCTGTATGCGACGCT 61.079 55.000 22.08 9.12 35.46 5.07
4043 4059 1.345176 GTTGCTCTGTATGCGACGC 59.655 57.895 14.19 14.19 35.46 5.19
4044 4060 0.366871 GTGTTGCTCTGTATGCGACG 59.633 55.000 0.00 0.00 45.18 5.12
4045 4061 0.721718 GGTGTTGCTCTGTATGCGAC 59.278 55.000 0.00 0.00 43.20 5.19
4046 4062 0.608130 AGGTGTTGCTCTGTATGCGA 59.392 50.000 0.00 0.00 0.00 5.10
4047 4063 1.394917 GAAGGTGTTGCTCTGTATGCG 59.605 52.381 0.00 0.00 0.00 4.73
4048 4064 2.426522 TGAAGGTGTTGCTCTGTATGC 58.573 47.619 0.00 0.00 0.00 3.14
4049 4065 4.318332 TCTTGAAGGTGTTGCTCTGTATG 58.682 43.478 0.00 0.00 0.00 2.39
4050 4066 4.623932 TCTTGAAGGTGTTGCTCTGTAT 57.376 40.909 0.00 0.00 0.00 2.29
4051 4067 4.380531 CTTCTTGAAGGTGTTGCTCTGTA 58.619 43.478 2.63 0.00 0.00 2.74
4052 4068 3.209410 CTTCTTGAAGGTGTTGCTCTGT 58.791 45.455 2.63 0.00 0.00 3.41
4053 4069 2.551459 CCTTCTTGAAGGTGTTGCTCTG 59.449 50.000 18.52 0.00 35.22 3.35
4054 4070 2.439507 TCCTTCTTGAAGGTGTTGCTCT 59.560 45.455 23.78 0.00 40.81 4.09
4055 4071 2.851195 TCCTTCTTGAAGGTGTTGCTC 58.149 47.619 23.78 0.00 40.81 4.26
4056 4072 3.297134 TTCCTTCTTGAAGGTGTTGCT 57.703 42.857 23.78 0.00 40.81 3.91
4057 4073 3.858503 GCATTCCTTCTTGAAGGTGTTGC 60.859 47.826 23.78 23.54 40.81 4.17
4058 4074 3.610114 CGCATTCCTTCTTGAAGGTGTTG 60.610 47.826 23.78 19.69 40.81 3.33
4059 4075 2.554032 CGCATTCCTTCTTGAAGGTGTT 59.446 45.455 23.78 10.91 40.81 3.32
4060 4076 2.154462 CGCATTCCTTCTTGAAGGTGT 58.846 47.619 23.78 13.74 40.81 4.16
4061 4077 2.160417 GTCGCATTCCTTCTTGAAGGTG 59.840 50.000 23.78 18.02 40.81 4.00
4062 4078 2.427506 GTCGCATTCCTTCTTGAAGGT 58.572 47.619 23.78 7.77 40.81 3.50
4063 4079 1.394917 CGTCGCATTCCTTCTTGAAGG 59.605 52.381 20.21 20.21 41.35 3.46
4064 4080 2.092838 GTCGTCGCATTCCTTCTTGAAG 59.907 50.000 3.55 3.55 0.00 3.02
4065 4081 2.066262 GTCGTCGCATTCCTTCTTGAA 58.934 47.619 0.00 0.00 0.00 2.69
4066 4082 1.710013 GTCGTCGCATTCCTTCTTGA 58.290 50.000 0.00 0.00 0.00 3.02
4067 4083 0.366871 CGTCGTCGCATTCCTTCTTG 59.633 55.000 0.00 0.00 0.00 3.02
4068 4084 0.242825 TCGTCGTCGCATTCCTTCTT 59.757 50.000 0.00 0.00 36.96 2.52
4069 4085 0.456312 GTCGTCGTCGCATTCCTTCT 60.456 55.000 0.00 0.00 36.96 2.85
4070 4086 1.730593 CGTCGTCGTCGCATTCCTTC 61.731 60.000 0.00 0.00 36.96 3.46
4071 4087 1.800315 CGTCGTCGTCGCATTCCTT 60.800 57.895 0.00 0.00 36.96 3.36
4072 4088 2.202440 CGTCGTCGTCGCATTCCT 60.202 61.111 0.00 0.00 36.96 3.36
4090 4106 4.641645 TTGTCCGGGCAGCAGTGG 62.642 66.667 9.61 0.00 0.00 4.00
4091 4107 3.052082 CTTGTCCGGGCAGCAGTG 61.052 66.667 9.61 0.00 0.00 3.66
4092 4108 3.537206 GACTTGTCCGGGCAGCAGT 62.537 63.158 13.16 13.16 0.00 4.40
4093 4109 2.743928 GACTTGTCCGGGCAGCAG 60.744 66.667 9.61 7.67 0.00 4.24
4094 4110 4.329545 GGACTTGTCCGGGCAGCA 62.330 66.667 9.61 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.