Multiple sequence alignment - TraesCS5A01G199200

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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 TraesCS5A01G199200 chr5A 100.000 3572 0 0 1 3572 404014914 404018485 0.000000e+00 6597.0
1 TraesCS5A01G199200 chr5A 73.966 411 95 11 1851 2255 385382566 385382162 4.770000e-34 156.0
2 TraesCS5A01G199200 chr5A 74.359 351 71 15 1851 2192 690357286 690356946 8.050000e-27 132.0
3 TraesCS5A01G199200 chr5B 94.894 1841 79 6 936 2772 356358807 356360636 0.000000e+00 2865.0
4 TraesCS5A01G199200 chr5B 95.506 801 15 2 1 781 169608343 169609142 0.000000e+00 1260.0
5 TraesCS5A01G199200 chr5B 92.491 799 33 9 2 776 622615319 622616114 0.000000e+00 1118.0
6 TraesCS5A01G199200 chr5B 92.240 799 35 5 2 776 691971639 691970844 0.000000e+00 1107.0
7 TraesCS5A01G199200 chr5B 92.419 277 15 1 3302 3572 356360945 356361221 1.200000e-104 390.0
8 TraesCS5A01G199200 chr5B 89.908 218 19 3 2770 2986 356360670 356360885 9.770000e-71 278.0
9 TraesCS5A01G199200 chr5B 71.741 1235 255 72 1077 2255 333196545 333195349 9.840000e-66 261.0
10 TraesCS5A01G199200 chr5B 94.656 131 6 1 779 908 356358678 356358808 6.050000e-48 202.0
11 TraesCS5A01G199200 chr5D 95.312 1472 66 1 981 2449 310496807 310498278 0.000000e+00 2333.0
12 TraesCS5A01G199200 chr5D 93.467 796 28 10 2 776 301120773 301121565 0.000000e+00 1160.0
13 TraesCS5A01G199200 chr5D 93.716 366 19 3 2659 3023 310501383 310501745 2.420000e-151 545.0
14 TraesCS5A01G199200 chr5D 96.310 271 8 2 3302 3572 310501743 310502011 9.100000e-121 444.0
15 TraesCS5A01G199200 chr5D 92.896 183 10 3 2474 2655 310498552 310498732 2.730000e-66 263.0
16 TraesCS5A01G199200 chr6B 96.020 804 11 2 1 784 213230301 213229499 0.000000e+00 1288.0
17 TraesCS5A01G199200 chr4A 95.755 801 13 2 1 781 738982520 738981721 0.000000e+00 1271.0
18 TraesCS5A01G199200 chr4A 95.264 739 13 3 62 780 618859028 618858292 0.000000e+00 1151.0
19 TraesCS5A01G199200 chr4A 92.085 796 38 5 2 776 712441078 712441869 0.000000e+00 1098.0
20 TraesCS5A01G199200 chr3A 93.116 799 32 3 1 779 532044934 532044139 0.000000e+00 1149.0
21 TraesCS5A01G199200 chr3A 92.616 799 36 13 1 779 532096240 532095445 0.000000e+00 1127.0
22 TraesCS5A01G199200 chr3A 92.115 799 40 7 1 779 532070141 532069346 0.000000e+00 1105.0
23 TraesCS5A01G199200 chr3A 90.526 285 22 4 3020 3304 605072952 605072673 4.360000e-99 372.0
24 TraesCS5A01G199200 chr3D 92.240 799 35 6 2 776 310716813 310716018 0.000000e+00 1107.0
25 TraesCS5A01G199200 chr1B 92.240 799 34 6 2 776 17627616 17628410 0.000000e+00 1107.0
26 TraesCS5A01G199200 chr1B 89.347 291 25 5 3017 3307 411392263 411392547 9.430000e-96 361.0
27 TraesCS5A01G199200 chr2D 92.690 725 29 4 2 705 133749451 133750172 0.000000e+00 1024.0
28 TraesCS5A01G199200 chrUn 89.333 300 26 5 3017 3315 36437103 36437397 4.360000e-99 372.0
29 TraesCS5A01G199200 chrUn 90.493 284 22 4 3021 3304 50077466 50077188 1.570000e-98 370.0
30 TraesCS5A01G199200 chr7D 91.544 272 18 3 3023 3294 2512242 2512508 1.570000e-98 370.0
31 TraesCS5A01G199200 chr1D 91.007 278 20 4 3023 3300 263874978 263875250 1.570000e-98 370.0
32 TraesCS5A01G199200 chr4D 90.647 278 22 3 3017 3294 287778911 287779184 2.030000e-97 366.0
33 TraesCS5A01G199200 chr4D 89.347 291 26 4 3017 3307 318830808 318831093 9.430000e-96 361.0
34 TraesCS5A01G199200 chr2B 88.889 297 26 6 3017 3312 36443808 36444098 3.390000e-95 359.0
35 TraesCS5A01G199200 chr4B 71.151 1182 276 56 1077 2215 652915600 652914441 2.140000e-57 233.0
36 TraesCS5A01G199200 chr7B 90.000 60 6 0 2118 2177 574486337 574486278 1.060000e-10 78.7
37 TraesCS5A01G199200 chr7B 90.000 50 5 0 2109 2158 136548309 136548358 8.280000e-07 65.8
38 TraesCS5A01G199200 chr7A 90.000 50 5 0 2109 2158 173409858 173409907 8.280000e-07 65.8


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 TraesCS5A01G199200 chr5A 404014914 404018485 3571 False 6597.00 6597 100.00000 1 3572 1 chr5A.!!$F1 3571
1 TraesCS5A01G199200 chr5B 169608343 169609142 799 False 1260.00 1260 95.50600 1 781 1 chr5B.!!$F1 780
2 TraesCS5A01G199200 chr5B 622615319 622616114 795 False 1118.00 1118 92.49100 2 776 1 chr5B.!!$F2 774
3 TraesCS5A01G199200 chr5B 691970844 691971639 795 True 1107.00 1107 92.24000 2 776 1 chr5B.!!$R2 774
4 TraesCS5A01G199200 chr5B 356358678 356361221 2543 False 933.75 2865 92.96925 779 3572 4 chr5B.!!$F3 2793
5 TraesCS5A01G199200 chr5B 333195349 333196545 1196 True 261.00 261 71.74100 1077 2255 1 chr5B.!!$R1 1178
6 TraesCS5A01G199200 chr5D 301120773 301121565 792 False 1160.00 1160 93.46700 2 776 1 chr5D.!!$F1 774
7 TraesCS5A01G199200 chr5D 310496807 310502011 5204 False 896.25 2333 94.55850 981 3572 4 chr5D.!!$F2 2591
8 TraesCS5A01G199200 chr6B 213229499 213230301 802 True 1288.00 1288 96.02000 1 784 1 chr6B.!!$R1 783
9 TraesCS5A01G199200 chr4A 738981721 738982520 799 True 1271.00 1271 95.75500 1 781 1 chr4A.!!$R2 780
10 TraesCS5A01G199200 chr4A 618858292 618859028 736 True 1151.00 1151 95.26400 62 780 1 chr4A.!!$R1 718
11 TraesCS5A01G199200 chr4A 712441078 712441869 791 False 1098.00 1098 92.08500 2 776 1 chr4A.!!$F1 774
12 TraesCS5A01G199200 chr3A 532044139 532044934 795 True 1149.00 1149 93.11600 1 779 1 chr3A.!!$R1 778
13 TraesCS5A01G199200 chr3A 532095445 532096240 795 True 1127.00 1127 92.61600 1 779 1 chr3A.!!$R3 778
14 TraesCS5A01G199200 chr3A 532069346 532070141 795 True 1105.00 1105 92.11500 1 779 1 chr3A.!!$R2 778
15 TraesCS5A01G199200 chr3D 310716018 310716813 795 True 1107.00 1107 92.24000 2 776 1 chr3D.!!$R1 774
16 TraesCS5A01G199200 chr1B 17627616 17628410 794 False 1107.00 1107 92.24000 2 776 1 chr1B.!!$F1 774
17 TraesCS5A01G199200 chr2D 133749451 133750172 721 False 1024.00 1024 92.69000 2 705 1 chr2D.!!$F1 703
18 TraesCS5A01G199200 chr4B 652914441 652915600 1159 True 233.00 233 71.15100 1077 2215 1 chr4B.!!$R1 1138

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
932 967 0.039256 CAGTGGGGTGACAATTTGCG 60.039 55.000 0.00 0.00 0.0 4.85 F
933 968 1.178534 AGTGGGGTGACAATTTGCGG 61.179 55.000 0.00 0.00 0.0 5.69 F
1433 1474 1.595357 GACGGGTTCCTGTACTGGG 59.405 63.158 17.82 8.78 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2115 0.557729 CTCCCATTACCATGCCCCTT 59.442 55.0 0.00 0.0 0.00 3.95 R
2260 2325 1.196104 CCTTGACCAACCCTCCGGTA 61.196 60.0 0.00 0.0 43.71 4.02 R
3249 6277 0.969149 ACATCGAGTCCAACTCAGCA 59.031 50.0 7.78 0.0 45.30 4.41 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
597 631 3.683885 AGGTGTGGTACATCTCCGA 57.316 52.632 0.00 0.00 33.49 4.55
856 891 3.120786 CCGTTCGTAATTCAGCGAAGTTT 60.121 43.478 11.09 0.00 45.81 2.66
859 894 2.158841 TCGTAATTCAGCGAAGTTTGCC 59.841 45.455 11.66 0.00 33.96 4.52
881 916 3.698040 CAGCTATGAGGGTCAAATTTGCT 59.302 43.478 13.54 4.95 0.00 3.91
904 939 2.817844 GTTTGGTCAAAGACGCCCTTAT 59.182 45.455 0.00 0.00 34.00 1.73
906 941 3.149005 TGGTCAAAGACGCCCTTATTT 57.851 42.857 0.00 0.00 34.00 1.40
907 942 3.492337 TGGTCAAAGACGCCCTTATTTT 58.508 40.909 0.00 0.00 34.00 1.82
908 943 3.254657 TGGTCAAAGACGCCCTTATTTTG 59.745 43.478 0.00 0.00 34.00 2.44
909 944 3.504520 GGTCAAAGACGCCCTTATTTTGA 59.495 43.478 0.00 0.00 35.93 2.69
910 945 4.157840 GGTCAAAGACGCCCTTATTTTGAT 59.842 41.667 1.88 0.00 39.21 2.57
911 946 5.095490 GTCAAAGACGCCCTTATTTTGATG 58.905 41.667 1.88 0.00 39.21 3.07
912 947 5.007034 TCAAAGACGCCCTTATTTTGATGA 58.993 37.500 0.00 0.00 34.04 2.92
913 948 4.965119 AAGACGCCCTTATTTTGATGAC 57.035 40.909 0.00 0.00 32.24 3.06
914 949 3.950397 AGACGCCCTTATTTTGATGACA 58.050 40.909 0.00 0.00 0.00 3.58
915 950 3.941483 AGACGCCCTTATTTTGATGACAG 59.059 43.478 0.00 0.00 0.00 3.51
916 951 3.686016 ACGCCCTTATTTTGATGACAGT 58.314 40.909 0.00 0.00 0.00 3.55
917 952 3.440173 ACGCCCTTATTTTGATGACAGTG 59.560 43.478 0.00 0.00 0.00 3.66
918 953 3.181497 CGCCCTTATTTTGATGACAGTGG 60.181 47.826 0.00 0.00 0.00 4.00
919 954 3.131046 GCCCTTATTTTGATGACAGTGGG 59.869 47.826 0.00 0.00 0.00 4.61
920 955 3.701040 CCCTTATTTTGATGACAGTGGGG 59.299 47.826 0.00 0.00 0.00 4.96
921 956 4.344104 CCTTATTTTGATGACAGTGGGGT 58.656 43.478 0.00 0.00 0.00 4.95
922 957 4.158394 CCTTATTTTGATGACAGTGGGGTG 59.842 45.833 0.00 0.00 0.00 4.61
923 958 3.524095 ATTTTGATGACAGTGGGGTGA 57.476 42.857 0.00 0.00 0.00 4.02
924 959 2.270352 TTTGATGACAGTGGGGTGAC 57.730 50.000 0.00 0.00 0.00 3.67
925 960 1.135960 TTGATGACAGTGGGGTGACA 58.864 50.000 0.00 0.00 0.00 3.58
926 961 1.135960 TGATGACAGTGGGGTGACAA 58.864 50.000 0.00 0.00 0.00 3.18
927 962 1.704628 TGATGACAGTGGGGTGACAAT 59.295 47.619 0.00 0.00 0.00 2.71
928 963 2.108075 TGATGACAGTGGGGTGACAATT 59.892 45.455 0.00 0.00 0.00 2.32
929 964 2.746279 TGACAGTGGGGTGACAATTT 57.254 45.000 0.00 0.00 0.00 1.82
930 965 2.305928 TGACAGTGGGGTGACAATTTG 58.694 47.619 0.00 0.00 0.00 2.32
931 966 1.000274 GACAGTGGGGTGACAATTTGC 60.000 52.381 0.00 0.00 0.00 3.68
932 967 0.039256 CAGTGGGGTGACAATTTGCG 60.039 55.000 0.00 0.00 0.00 4.85
933 968 1.178534 AGTGGGGTGACAATTTGCGG 61.179 55.000 0.00 0.00 0.00 5.69
934 969 1.905843 TGGGGTGACAATTTGCGGG 60.906 57.895 0.00 0.00 0.00 6.13
1041 1076 1.809651 GCAGAGAAGCATGGCTCCTAC 60.810 57.143 0.00 0.00 38.25 3.18
1213 1248 4.347453 AACGCGGCCTTCGTACGT 62.347 61.111 18.15 7.50 39.48 3.57
1304 1345 2.401766 GCGGAGAACGTCGAGGGTA 61.402 63.158 10.27 0.00 46.52 3.69
1433 1474 1.595357 GACGGGTTCCTGTACTGGG 59.405 63.158 17.82 8.78 0.00 4.45
1633 1677 2.348998 CTGCTGGCCGATATCCCC 59.651 66.667 0.00 0.00 0.00 4.81
1681 1743 2.025156 GCAAAGATGGCGATGGCG 59.975 61.111 0.00 0.00 41.24 5.69
1847 1909 2.354805 GGCGAAGTCCATAACTCCAAGT 60.355 50.000 0.00 0.00 37.17 3.16
2260 2325 1.908793 CGGTGTCAGGGTCAGGTCT 60.909 63.158 0.00 0.00 0.00 3.85
2266 2331 1.000019 CAGGGTCAGGTCTACCGGA 60.000 63.158 9.46 0.00 42.08 5.14
2340 2405 4.309950 GACAAGGGTGTCGGCGGT 62.310 66.667 7.21 0.00 44.58 5.68
2357 2422 3.039588 TGAAGAACGCGGCGGTTC 61.040 61.111 27.37 24.28 45.19 3.62
2486 2800 3.000815 CACGTTGGTGGCAAGTAGT 57.999 52.632 0.00 0.00 40.58 2.73
2520 2834 7.628769 TGAAGAAATATGAGCAATGTAGCAA 57.371 32.000 0.00 0.00 36.85 3.91
2521 2835 7.700505 TGAAGAAATATGAGCAATGTAGCAAG 58.299 34.615 0.00 0.00 36.85 4.01
2544 2859 8.395633 CAAGTCCGGAAACCTATTGTAAAATAG 58.604 37.037 5.23 5.75 33.58 1.73
2560 2875 8.630054 TGTAAAATAGCTAGGTGTGATGTTTT 57.370 30.769 4.27 0.71 0.00 2.43
2593 2908 6.906157 AAGATCAATGTCAACATGGAACTT 57.094 33.333 14.13 14.13 41.62 2.66
2594 2909 6.906157 AGATCAATGTCAACATGGAACTTT 57.094 33.333 4.37 0.00 39.55 2.66
2615 2930 7.365741 ACTTTGGTATCTGGTTACGTATATCG 58.634 38.462 0.00 0.00 46.00 2.92
2655 2970 5.935945 TGTTATTGGTTCTGGTCTTTCTCA 58.064 37.500 0.00 0.00 0.00 3.27
2656 2971 6.542821 TGTTATTGGTTCTGGTCTTTCTCAT 58.457 36.000 0.00 0.00 0.00 2.90
2657 2972 6.655003 TGTTATTGGTTCTGGTCTTTCTCATC 59.345 38.462 0.00 0.00 0.00 2.92
2672 5634 5.927281 TTCTCATCATCTCATGTGACTGA 57.073 39.130 0.00 6.09 0.00 3.41
2893 5894 2.943033 TGAGTGATCATCGACGAAGCTA 59.057 45.455 0.00 0.00 0.00 3.32
2900 5901 3.966154 TCATCGACGAAGCTATTCCTTC 58.034 45.455 0.00 0.00 38.24 3.46
2951 5953 4.612412 TTTCGAGCAACCGGCCGT 62.612 61.111 26.12 9.63 46.50 5.68
2994 5996 1.001406 AGAAGAGAGAAACAGGCACCG 59.999 52.381 0.00 0.00 0.00 4.94
2999 6027 1.141053 AGAGAAACAGGCACCGAGTTT 59.859 47.619 11.43 11.43 38.10 2.66
3024 6052 2.169832 CTCCAAACGGAGCTTTGAGA 57.830 50.000 0.00 0.00 43.69 3.27
3025 6053 1.801178 CTCCAAACGGAGCTTTGAGAC 59.199 52.381 0.00 0.00 43.69 3.36
3026 6054 1.416401 TCCAAACGGAGCTTTGAGACT 59.584 47.619 0.00 0.00 32.92 3.24
3027 6055 2.631062 TCCAAACGGAGCTTTGAGACTA 59.369 45.455 0.00 0.00 32.92 2.59
3028 6056 2.996621 CCAAACGGAGCTTTGAGACTAG 59.003 50.000 0.00 0.00 32.92 2.57
3029 6057 2.371910 AACGGAGCTTTGAGACTAGC 57.628 50.000 0.00 0.00 37.66 3.42
3030 6058 0.533032 ACGGAGCTTTGAGACTAGCC 59.467 55.000 0.00 0.00 38.14 3.93
3031 6059 0.532573 CGGAGCTTTGAGACTAGCCA 59.467 55.000 0.00 0.00 38.14 4.75
3032 6060 1.137872 CGGAGCTTTGAGACTAGCCAT 59.862 52.381 0.00 0.00 38.14 4.40
3033 6061 2.362397 CGGAGCTTTGAGACTAGCCATA 59.638 50.000 0.00 0.00 38.14 2.74
3034 6062 3.181475 CGGAGCTTTGAGACTAGCCATAA 60.181 47.826 0.00 0.00 38.14 1.90
3035 6063 4.502259 CGGAGCTTTGAGACTAGCCATAAT 60.502 45.833 0.00 0.00 38.14 1.28
3036 6064 4.754114 GGAGCTTTGAGACTAGCCATAATG 59.246 45.833 0.00 0.00 38.14 1.90
3037 6065 5.453903 GGAGCTTTGAGACTAGCCATAATGA 60.454 44.000 0.00 0.00 38.14 2.57
3038 6066 5.994250 AGCTTTGAGACTAGCCATAATGAA 58.006 37.500 0.00 0.00 38.14 2.57
3039 6067 6.054295 AGCTTTGAGACTAGCCATAATGAAG 58.946 40.000 0.00 0.00 38.14 3.02
3040 6068 6.051717 GCTTTGAGACTAGCCATAATGAAGA 58.948 40.000 0.00 0.00 0.00 2.87
3041 6069 6.202570 GCTTTGAGACTAGCCATAATGAAGAG 59.797 42.308 0.00 0.00 0.00 2.85
3042 6070 6.798427 TTGAGACTAGCCATAATGAAGAGT 57.202 37.500 0.00 0.00 0.00 3.24
3043 6071 7.898014 TTGAGACTAGCCATAATGAAGAGTA 57.102 36.000 0.00 0.00 0.00 2.59
3044 6072 7.898014 TGAGACTAGCCATAATGAAGAGTAA 57.102 36.000 0.00 0.00 0.00 2.24
3045 6073 7.717568 TGAGACTAGCCATAATGAAGAGTAAC 58.282 38.462 0.00 0.00 0.00 2.50
3046 6074 7.342026 TGAGACTAGCCATAATGAAGAGTAACA 59.658 37.037 0.00 0.00 0.00 2.41
3047 6075 8.256356 AGACTAGCCATAATGAAGAGTAACAT 57.744 34.615 0.00 0.00 0.00 2.71
3048 6076 9.368416 AGACTAGCCATAATGAAGAGTAACATA 57.632 33.333 0.00 0.00 0.00 2.29
3104 6132 8.234136 TGTTACTATCTTCATACAGTAGTGGG 57.766 38.462 1.92 0.00 0.00 4.61
3105 6133 7.837689 TGTTACTATCTTCATACAGTAGTGGGT 59.162 37.037 1.92 0.00 0.00 4.51
3106 6134 9.347240 GTTACTATCTTCATACAGTAGTGGGTA 57.653 37.037 1.92 0.00 0.00 3.69
3107 6135 9.570468 TTACTATCTTCATACAGTAGTGGGTAG 57.430 37.037 1.92 0.00 0.00 3.18
3108 6136 7.584532 ACTATCTTCATACAGTAGTGGGTAGT 58.415 38.462 1.92 0.00 0.00 2.73
3109 6137 8.721479 ACTATCTTCATACAGTAGTGGGTAGTA 58.279 37.037 1.92 0.00 0.00 1.82
3110 6138 9.570468 CTATCTTCATACAGTAGTGGGTAGTAA 57.430 37.037 1.92 0.00 0.00 2.24
3111 6139 7.636150 TCTTCATACAGTAGTGGGTAGTAAC 57.364 40.000 1.92 0.00 0.00 2.50
3112 6140 7.177184 TCTTCATACAGTAGTGGGTAGTAACA 58.823 38.462 1.92 0.00 0.00 2.41
3113 6141 7.837689 TCTTCATACAGTAGTGGGTAGTAACAT 59.162 37.037 1.92 0.00 0.00 2.71
3114 6142 9.128404 CTTCATACAGTAGTGGGTAGTAACATA 57.872 37.037 1.92 0.00 0.00 2.29
3115 6143 9.478238 TTCATACAGTAGTGGGTAGTAACATAA 57.522 33.333 1.92 0.00 0.00 1.90
3116 6144 9.128404 TCATACAGTAGTGGGTAGTAACATAAG 57.872 37.037 1.92 0.00 0.00 1.73
3117 6145 6.218108 ACAGTAGTGGGTAGTAACATAAGC 57.782 41.667 1.92 0.00 0.00 3.09
3118 6146 5.718130 ACAGTAGTGGGTAGTAACATAAGCA 59.282 40.000 1.92 0.00 0.00 3.91
3119 6147 6.383147 ACAGTAGTGGGTAGTAACATAAGCAT 59.617 38.462 1.92 0.00 0.00 3.79
3120 6148 6.701841 CAGTAGTGGGTAGTAACATAAGCATG 59.298 42.308 0.00 0.00 38.21 4.06
3121 6149 5.036117 AGTGGGTAGTAACATAAGCATGG 57.964 43.478 0.00 0.00 36.39 3.66
3122 6150 4.473559 AGTGGGTAGTAACATAAGCATGGT 59.526 41.667 0.00 0.00 36.39 3.55
3123 6151 5.664006 AGTGGGTAGTAACATAAGCATGGTA 59.336 40.000 0.00 0.00 36.39 3.25
3124 6152 6.157297 AGTGGGTAGTAACATAAGCATGGTAA 59.843 38.462 0.00 0.00 36.09 2.85
3125 6153 6.259387 GTGGGTAGTAACATAAGCATGGTAAC 59.741 42.308 0.00 0.00 36.09 2.50
3140 6168 4.870123 TGGTAACATGCAAAGCTTCATT 57.130 36.364 0.00 0.00 46.17 2.57
3141 6169 5.212532 TGGTAACATGCAAAGCTTCATTT 57.787 34.783 0.00 1.04 46.17 2.32
3142 6170 6.338214 TGGTAACATGCAAAGCTTCATTTA 57.662 33.333 0.00 0.18 46.17 1.40
3143 6171 6.934056 TGGTAACATGCAAAGCTTCATTTAT 58.066 32.000 0.00 0.00 46.17 1.40
3144 6172 7.385267 TGGTAACATGCAAAGCTTCATTTATT 58.615 30.769 0.00 0.00 46.17 1.40
3145 6173 8.526978 TGGTAACATGCAAAGCTTCATTTATTA 58.473 29.630 0.00 0.00 46.17 0.98
3146 6174 9.533253 GGTAACATGCAAAGCTTCATTTATTAT 57.467 29.630 0.00 0.00 0.00 1.28
3149 6177 9.439500 AACATGCAAAGCTTCATTTATTATGTT 57.561 25.926 0.00 6.25 31.49 2.71
3170 6198 7.439157 TGTTATAGACTCATATTGCATTGGC 57.561 36.000 0.00 0.00 41.68 4.52
3182 6210 2.373540 GCATTGGCACATGTGATGTT 57.626 45.000 29.80 7.93 42.70 2.71
3183 6211 2.264813 GCATTGGCACATGTGATGTTC 58.735 47.619 29.80 10.82 42.70 3.18
3184 6212 2.883574 CATTGGCACATGTGATGTTCC 58.116 47.619 29.80 19.60 45.23 3.62
3187 6215 1.538047 GGCACATGTGATGTTCCAGT 58.462 50.000 29.80 0.00 44.53 4.00
3188 6216 2.710377 GGCACATGTGATGTTCCAGTA 58.290 47.619 29.80 0.00 44.53 2.74
3189 6217 3.081061 GGCACATGTGATGTTCCAGTAA 58.919 45.455 29.80 0.00 44.53 2.24
3190 6218 3.119849 GGCACATGTGATGTTCCAGTAAC 60.120 47.826 29.80 6.38 44.53 2.50
3191 6219 3.753272 GCACATGTGATGTTCCAGTAACT 59.247 43.478 29.80 0.00 42.70 2.24
3192 6220 4.935205 GCACATGTGATGTTCCAGTAACTA 59.065 41.667 29.80 0.00 42.70 2.24
3193 6221 5.063944 GCACATGTGATGTTCCAGTAACTAG 59.936 44.000 29.80 0.00 42.70 2.57
3194 6222 5.063944 CACATGTGATGTTCCAGTAACTAGC 59.936 44.000 21.64 0.00 42.70 3.42
3195 6223 5.046304 ACATGTGATGTTCCAGTAACTAGCT 60.046 40.000 0.00 0.00 41.63 3.32
3196 6224 6.154534 ACATGTGATGTTCCAGTAACTAGCTA 59.845 38.462 0.00 0.00 41.63 3.32
3197 6225 6.599356 TGTGATGTTCCAGTAACTAGCTAA 57.401 37.500 0.00 0.00 38.99 3.09
3198 6226 6.631016 TGTGATGTTCCAGTAACTAGCTAAG 58.369 40.000 0.00 0.00 38.99 2.18
3199 6227 6.210784 TGTGATGTTCCAGTAACTAGCTAAGT 59.789 38.462 0.00 0.00 41.49 2.24
3201 6229 8.248945 GTGATGTTCCAGTAACTAGCTAAGTTA 58.751 37.037 10.09 10.09 46.85 2.24
3215 6243 9.683870 ACTAGCTAAGTTACTACAACTACATCT 57.316 33.333 0.00 0.00 33.35 2.90
3217 6245 8.810990 AGCTAAGTTACTACAACTACATCTCT 57.189 34.615 0.00 0.00 0.00 3.10
3218 6246 8.895737 AGCTAAGTTACTACAACTACATCTCTC 58.104 37.037 0.00 0.00 0.00 3.20
3219 6247 8.130469 GCTAAGTTACTACAACTACATCTCTCC 58.870 40.741 0.00 0.00 0.00 3.71
3220 6248 9.398538 CTAAGTTACTACAACTACATCTCTCCT 57.601 37.037 0.00 0.00 0.00 3.69
3221 6249 7.868906 AGTTACTACAACTACATCTCTCCTC 57.131 40.000 0.00 0.00 0.00 3.71
3222 6250 7.403671 AGTTACTACAACTACATCTCTCCTCA 58.596 38.462 0.00 0.00 0.00 3.86
3223 6251 7.889073 AGTTACTACAACTACATCTCTCCTCAA 59.111 37.037 0.00 0.00 0.00 3.02
3224 6252 8.688151 GTTACTACAACTACATCTCTCCTCAAT 58.312 37.037 0.00 0.00 0.00 2.57
3225 6253 9.916360 TTACTACAACTACATCTCTCCTCAATA 57.084 33.333 0.00 0.00 0.00 1.90
3226 6254 8.824756 ACTACAACTACATCTCTCCTCAATAA 57.175 34.615 0.00 0.00 0.00 1.40
3227 6255 8.688151 ACTACAACTACATCTCTCCTCAATAAC 58.312 37.037 0.00 0.00 0.00 1.89
3228 6256 7.726033 ACAACTACATCTCTCCTCAATAACT 57.274 36.000 0.00 0.00 0.00 2.24
3229 6257 7.777095 ACAACTACATCTCTCCTCAATAACTC 58.223 38.462 0.00 0.00 0.00 3.01
3230 6258 7.397476 ACAACTACATCTCTCCTCAATAACTCA 59.603 37.037 0.00 0.00 0.00 3.41
3231 6259 8.420222 CAACTACATCTCTCCTCAATAACTCAT 58.580 37.037 0.00 0.00 0.00 2.90
3232 6260 8.546083 ACTACATCTCTCCTCAATAACTCATT 57.454 34.615 0.00 0.00 0.00 2.57
3233 6261 8.420222 ACTACATCTCTCCTCAATAACTCATTG 58.580 37.037 0.00 0.00 44.69 2.82
3234 6262 6.590068 ACATCTCTCCTCAATAACTCATTGG 58.410 40.000 0.00 0.00 43.68 3.16
3235 6263 5.028549 TCTCTCCTCAATAACTCATTGGC 57.971 43.478 0.00 0.00 43.68 4.52
3236 6264 4.471025 TCTCTCCTCAATAACTCATTGGCA 59.529 41.667 0.00 0.00 43.68 4.92
3237 6265 4.517285 TCTCCTCAATAACTCATTGGCAC 58.483 43.478 0.00 0.00 43.68 5.01
3238 6266 4.019411 TCTCCTCAATAACTCATTGGCACA 60.019 41.667 0.00 0.00 43.68 4.57
3239 6267 4.858850 TCCTCAATAACTCATTGGCACAT 58.141 39.130 0.00 0.00 43.68 3.21
3240 6268 6.000246 TCCTCAATAACTCATTGGCACATA 58.000 37.500 0.00 0.00 43.68 2.29
3241 6269 6.422333 TCCTCAATAACTCATTGGCACATAA 58.578 36.000 0.00 0.00 43.68 1.90
3242 6270 6.543465 TCCTCAATAACTCATTGGCACATAAG 59.457 38.462 0.00 0.00 43.68 1.73
3243 6271 6.135290 TCAATAACTCATTGGCACATAAGC 57.865 37.500 0.00 0.00 43.68 3.09
3244 6272 5.651576 TCAATAACTCATTGGCACATAAGCA 59.348 36.000 0.00 0.00 43.68 3.91
3245 6273 6.152492 TCAATAACTCATTGGCACATAAGCAA 59.848 34.615 0.00 0.00 43.68 3.91
3246 6274 4.870123 AACTCATTGGCACATAAGCAAA 57.130 36.364 0.00 0.00 39.30 3.68
3247 6275 5.410355 AACTCATTGGCACATAAGCAAAT 57.590 34.783 0.00 0.00 38.67 2.32
3248 6276 5.410355 ACTCATTGGCACATAAGCAAATT 57.590 34.783 0.00 0.00 36.01 1.82
3249 6277 5.797051 ACTCATTGGCACATAAGCAAATTT 58.203 33.333 0.00 0.00 36.01 1.82
3250 6278 5.640357 ACTCATTGGCACATAAGCAAATTTG 59.360 36.000 14.03 14.03 36.01 2.32
3274 6302 2.924290 GAGTTGGACTCGATGTTACTGC 59.076 50.000 0.00 0.00 35.28 4.40
3275 6303 2.563179 AGTTGGACTCGATGTTACTGCT 59.437 45.455 0.00 0.00 0.00 4.24
3276 6304 2.654749 TGGACTCGATGTTACTGCTG 57.345 50.000 0.00 0.00 0.00 4.41
3277 6305 2.167662 TGGACTCGATGTTACTGCTGA 58.832 47.619 0.00 0.00 0.00 4.26
3278 6306 2.560981 TGGACTCGATGTTACTGCTGAA 59.439 45.455 0.00 0.00 0.00 3.02
3279 6307 3.182967 GGACTCGATGTTACTGCTGAAG 58.817 50.000 0.00 0.00 0.00 3.02
3280 6308 3.367498 GGACTCGATGTTACTGCTGAAGT 60.367 47.826 0.00 0.00 43.40 3.01
3281 6309 4.238514 GACTCGATGTTACTGCTGAAGTT 58.761 43.478 0.00 0.00 40.56 2.66
3282 6310 5.386958 ACTCGATGTTACTGCTGAAGTTA 57.613 39.130 0.00 0.00 40.56 2.24
3283 6311 5.162075 ACTCGATGTTACTGCTGAAGTTAC 58.838 41.667 0.00 0.00 40.56 2.50
3284 6312 5.047943 ACTCGATGTTACTGCTGAAGTTACT 60.048 40.000 6.50 0.00 38.87 2.24
3285 6313 5.399858 TCGATGTTACTGCTGAAGTTACTC 58.600 41.667 6.50 1.79 38.87 2.59
3286 6314 4.563184 CGATGTTACTGCTGAAGTTACTCC 59.437 45.833 6.50 0.00 38.87 3.85
3287 6315 4.267349 TGTTACTGCTGAAGTTACTCCC 57.733 45.455 6.50 0.00 38.87 4.30
3288 6316 3.644265 TGTTACTGCTGAAGTTACTCCCA 59.356 43.478 6.50 0.00 38.87 4.37
3289 6317 4.286032 TGTTACTGCTGAAGTTACTCCCAT 59.714 41.667 6.50 0.00 38.87 4.00
3290 6318 5.221843 TGTTACTGCTGAAGTTACTCCCATT 60.222 40.000 6.50 0.00 38.87 3.16
3291 6319 3.679389 ACTGCTGAAGTTACTCCCATTG 58.321 45.455 0.00 0.00 34.57 2.82
3292 6320 3.073062 ACTGCTGAAGTTACTCCCATTGT 59.927 43.478 0.00 0.00 34.57 2.71
3293 6321 3.411446 TGCTGAAGTTACTCCCATTGTG 58.589 45.455 0.00 0.00 0.00 3.33
3294 6322 3.072330 TGCTGAAGTTACTCCCATTGTGA 59.928 43.478 0.00 0.00 0.00 3.58
3295 6323 3.437049 GCTGAAGTTACTCCCATTGTGAC 59.563 47.826 0.00 0.00 0.00 3.67
3296 6324 4.641396 CTGAAGTTACTCCCATTGTGACA 58.359 43.478 0.00 0.00 0.00 3.58
3297 6325 5.042463 TGAAGTTACTCCCATTGTGACAA 57.958 39.130 0.00 0.00 0.00 3.18
3298 6326 5.063204 TGAAGTTACTCCCATTGTGACAAG 58.937 41.667 3.74 0.00 0.00 3.16
3299 6327 4.706842 AGTTACTCCCATTGTGACAAGT 57.293 40.909 3.74 0.00 0.00 3.16
3300 6328 4.389374 AGTTACTCCCATTGTGACAAGTG 58.611 43.478 3.74 2.81 0.00 3.16
3445 6473 7.387122 ACGATGACATCATTATTCTCATTGAGG 59.613 37.037 15.58 0.00 36.57 3.86
3455 6483 8.491152 CATTATTCTCATTGAGGAACACGATAC 58.509 37.037 13.59 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
303 324 2.280524 CAAGCCACCCACGAACGA 60.281 61.111 0.14 0.00 0.00 3.85
597 631 2.338257 CAAAACCGTTGCGCCCAT 59.662 55.556 4.18 0.00 0.00 4.00
682 716 3.003740 GCACAAGCATGCCCAAAAA 57.996 47.368 15.66 0.00 39.86 1.94
796 830 3.486383 AGTTGTAGTGGGGTGACAATTG 58.514 45.455 3.24 3.24 35.65 2.32
856 891 0.991146 TTTGACCCTCATAGCTGGCA 59.009 50.000 0.00 0.00 0.00 4.92
859 894 3.698040 AGCAAATTTGACCCTCATAGCTG 59.302 43.478 22.31 0.00 0.00 4.24
881 916 1.104577 GGGCGTCTTTGACCAAACCA 61.105 55.000 0.00 0.00 36.84 3.67
904 939 2.092158 TGTCACCCCACTGTCATCAAAA 60.092 45.455 0.00 0.00 0.00 2.44
906 941 1.135960 TGTCACCCCACTGTCATCAA 58.864 50.000 0.00 0.00 0.00 2.57
907 942 1.135960 TTGTCACCCCACTGTCATCA 58.864 50.000 0.00 0.00 0.00 3.07
908 943 2.496899 ATTGTCACCCCACTGTCATC 57.503 50.000 0.00 0.00 0.00 2.92
909 944 2.892852 CAAATTGTCACCCCACTGTCAT 59.107 45.455 0.00 0.00 0.00 3.06
910 945 2.305928 CAAATTGTCACCCCACTGTCA 58.694 47.619 0.00 0.00 0.00 3.58
911 946 1.000274 GCAAATTGTCACCCCACTGTC 60.000 52.381 0.00 0.00 0.00 3.51
912 947 1.039856 GCAAATTGTCACCCCACTGT 58.960 50.000 0.00 0.00 0.00 3.55
913 948 0.039256 CGCAAATTGTCACCCCACTG 60.039 55.000 0.00 0.00 0.00 3.66
914 949 1.178534 CCGCAAATTGTCACCCCACT 61.179 55.000 0.00 0.00 0.00 4.00
915 950 1.288752 CCGCAAATTGTCACCCCAC 59.711 57.895 0.00 0.00 0.00 4.61
916 951 1.905843 CCCGCAAATTGTCACCCCA 60.906 57.895 0.00 0.00 0.00 4.96
917 952 1.468506 AACCCGCAAATTGTCACCCC 61.469 55.000 0.00 0.00 0.00 4.95
918 953 0.038618 GAACCCGCAAATTGTCACCC 60.039 55.000 0.00 0.00 0.00 4.61
919 954 0.958822 AGAACCCGCAAATTGTCACC 59.041 50.000 0.00 0.00 0.00 4.02
920 955 1.068541 GGAGAACCCGCAAATTGTCAC 60.069 52.381 0.00 0.00 0.00 3.67
921 956 1.243902 GGAGAACCCGCAAATTGTCA 58.756 50.000 0.00 0.00 0.00 3.58
933 968 5.642165 TGTATACATAGAGGAGGGAGAACC 58.358 45.833 0.08 0.00 40.67 3.62
934 969 5.184287 GCTGTATACATAGAGGAGGGAGAAC 59.816 48.000 5.91 0.00 0.00 3.01
1041 1076 0.395311 ATCACATGGAAGGGCAGCAG 60.395 55.000 0.00 0.00 0.00 4.24
1121 1156 4.394712 CAGGTGGGTGAGCGGGAC 62.395 72.222 0.00 0.00 0.00 4.46
1304 1345 4.814294 GGAGGACGCCGACGCAAT 62.814 66.667 0.00 0.00 45.53 3.56
1419 1460 2.267961 CGGCCCAGTACAGGAACC 59.732 66.667 5.75 6.10 0.00 3.62
1827 1889 2.930682 GACTTGGAGTTATGGACTTCGC 59.069 50.000 0.00 0.00 39.19 4.70
2012 2077 1.964223 GAATCCTATGCCGAGGTCAGA 59.036 52.381 1.19 0.00 37.88 3.27
2050 2115 0.557729 CTCCCATTACCATGCCCCTT 59.442 55.000 0.00 0.00 0.00 3.95
2089 2154 4.509756 CAGTCGTGCTGGAGGATG 57.490 61.111 0.00 0.00 41.42 3.51
2224 2289 4.062293 CACCGACCTTAAGTTCATCAACA 58.938 43.478 0.97 0.00 34.60 3.33
2260 2325 1.196104 CCTTGACCAACCCTCCGGTA 61.196 60.000 0.00 0.00 43.71 4.02
2266 2331 1.427072 CCTCACCCTTGACCAACCCT 61.427 60.000 0.00 0.00 0.00 4.34
2340 2405 3.039588 GAACCGCCGCGTTCTTCA 61.040 61.111 12.58 0.00 39.27 3.02
2486 2800 7.998580 TGCTCATATTTCTTCATTGCACATAA 58.001 30.769 0.00 0.00 0.00 1.90
2520 2834 6.541278 GCTATTTTACAATAGGTTTCCGGACT 59.459 38.462 1.83 0.00 41.64 3.85
2521 2835 6.541278 AGCTATTTTACAATAGGTTTCCGGAC 59.459 38.462 1.83 0.00 46.97 4.79
2544 2859 2.665519 CGCACAAAACATCACACCTAGC 60.666 50.000 0.00 0.00 0.00 3.42
2560 2875 6.072783 TGTTGACATTGATCTTTATTCGCACA 60.073 34.615 0.00 0.00 0.00 4.57
2593 2908 6.003326 TCCGATATACGTAACCAGATACCAA 58.997 40.000 0.00 0.00 40.78 3.67
2594 2909 5.559770 TCCGATATACGTAACCAGATACCA 58.440 41.667 0.00 0.00 40.78 3.25
2615 2930 5.695851 ATAACAAATCCGCAGAATCATCC 57.304 39.130 0.00 0.00 0.00 3.51
2893 5894 3.057033 GCTCATGTGCACTTTGAAGGAAT 60.057 43.478 19.41 0.00 0.00 3.01
2900 5901 2.984471 GTTGATGCTCATGTGCACTTTG 59.016 45.455 23.59 15.39 46.33 2.77
2932 5934 2.254350 GGCCGGTTGCTCGAAAAC 59.746 61.111 1.90 2.70 40.92 2.43
2951 5953 1.663643 CGTAATGAAAAGGCAGCGCTA 59.336 47.619 10.99 0.00 0.00 4.26
3006 6034 1.416401 AGTCTCAAAGCTCCGTTTGGA 59.584 47.619 0.00 0.00 43.88 3.53
3015 6043 5.620738 TCATTATGGCTAGTCTCAAAGCT 57.379 39.130 0.00 0.00 38.80 3.74
3018 6046 7.187824 ACTCTTCATTATGGCTAGTCTCAAA 57.812 36.000 0.00 0.00 0.00 2.69
3020 6048 7.342026 TGTTACTCTTCATTATGGCTAGTCTCA 59.658 37.037 0.00 0.00 0.00 3.27
3021 6049 7.717568 TGTTACTCTTCATTATGGCTAGTCTC 58.282 38.462 0.00 0.00 0.00 3.36
3022 6050 7.661536 TGTTACTCTTCATTATGGCTAGTCT 57.338 36.000 0.00 0.00 0.00 3.24
3078 6106 8.861086 CCCACTACTGTATGAAGATAGTAACAT 58.139 37.037 0.00 0.00 0.00 2.71
3079 6107 7.837689 ACCCACTACTGTATGAAGATAGTAACA 59.162 37.037 0.00 0.00 0.00 2.41
3080 6108 8.235359 ACCCACTACTGTATGAAGATAGTAAC 57.765 38.462 0.00 0.00 0.00 2.50
3081 6109 9.570468 CTACCCACTACTGTATGAAGATAGTAA 57.430 37.037 0.00 0.00 0.00 2.24
3082 6110 8.721479 ACTACCCACTACTGTATGAAGATAGTA 58.279 37.037 0.00 0.00 0.00 1.82
3083 6111 7.584532 ACTACCCACTACTGTATGAAGATAGT 58.415 38.462 0.00 0.00 0.00 2.12
3084 6112 9.570468 TTACTACCCACTACTGTATGAAGATAG 57.430 37.037 0.00 0.00 0.00 2.08
3085 6113 9.347240 GTTACTACCCACTACTGTATGAAGATA 57.653 37.037 0.00 0.00 0.00 1.98
3086 6114 7.837689 TGTTACTACCCACTACTGTATGAAGAT 59.162 37.037 0.00 0.00 0.00 2.40
3087 6115 7.177184 TGTTACTACCCACTACTGTATGAAGA 58.823 38.462 0.00 0.00 0.00 2.87
3088 6116 7.400599 TGTTACTACCCACTACTGTATGAAG 57.599 40.000 0.00 0.00 0.00 3.02
3089 6117 7.966339 ATGTTACTACCCACTACTGTATGAA 57.034 36.000 0.00 0.00 0.00 2.57
3090 6118 9.128404 CTTATGTTACTACCCACTACTGTATGA 57.872 37.037 0.00 0.00 0.00 2.15
3091 6119 7.866393 GCTTATGTTACTACCCACTACTGTATG 59.134 40.741 0.00 0.00 0.00 2.39
3092 6120 7.562454 TGCTTATGTTACTACCCACTACTGTAT 59.438 37.037 0.00 0.00 0.00 2.29
3093 6121 6.891361 TGCTTATGTTACTACCCACTACTGTA 59.109 38.462 0.00 0.00 0.00 2.74
3094 6122 5.718130 TGCTTATGTTACTACCCACTACTGT 59.282 40.000 0.00 0.00 0.00 3.55
3095 6123 6.216801 TGCTTATGTTACTACCCACTACTG 57.783 41.667 0.00 0.00 0.00 2.74
3096 6124 6.183360 CCATGCTTATGTTACTACCCACTACT 60.183 42.308 0.00 0.00 0.00 2.57
3097 6125 5.989777 CCATGCTTATGTTACTACCCACTAC 59.010 44.000 0.00 0.00 0.00 2.73
3098 6126 5.664006 ACCATGCTTATGTTACTACCCACTA 59.336 40.000 0.00 0.00 0.00 2.74
3099 6127 4.473559 ACCATGCTTATGTTACTACCCACT 59.526 41.667 0.00 0.00 0.00 4.00
3100 6128 4.777463 ACCATGCTTATGTTACTACCCAC 58.223 43.478 0.00 0.00 0.00 4.61
3101 6129 6.070136 TGTTACCATGCTTATGTTACTACCCA 60.070 38.462 0.00 0.00 0.00 4.51
3102 6130 6.350906 TGTTACCATGCTTATGTTACTACCC 58.649 40.000 0.00 0.00 0.00 3.69
3103 6131 7.861630 CATGTTACCATGCTTATGTTACTACC 58.138 38.462 0.00 0.00 41.88 3.18
3118 6146 5.410355 AATGAAGCTTTGCATGTTACCAT 57.590 34.783 0.00 0.00 0.00 3.55
3119 6147 4.870123 AATGAAGCTTTGCATGTTACCA 57.130 36.364 0.00 0.00 0.00 3.25
3120 6148 7.832503 AATAAATGAAGCTTTGCATGTTACC 57.167 32.000 0.00 0.00 0.00 2.85
3123 6151 9.439500 AACATAATAAATGAAGCTTTGCATGTT 57.561 25.926 0.00 5.96 0.00 2.71
3144 6172 9.166173 GCCAATGCAATATGAGTCTATAACATA 57.834 33.333 0.00 0.00 37.47 2.29
3145 6173 7.666804 TGCCAATGCAATATGAGTCTATAACAT 59.333 33.333 0.00 0.00 46.66 2.71
3146 6174 6.997476 TGCCAATGCAATATGAGTCTATAACA 59.003 34.615 0.00 0.00 46.66 2.41
3147 6175 7.439157 TGCCAATGCAATATGAGTCTATAAC 57.561 36.000 0.00 0.00 46.66 1.89
3163 6191 2.264813 GAACATCACATGTGCCAATGC 58.735 47.619 21.38 4.72 44.07 3.56
3169 6197 3.753272 AGTTACTGGAACATCACATGTGC 59.247 43.478 21.38 6.41 44.07 4.57
3170 6198 5.063944 GCTAGTTACTGGAACATCACATGTG 59.936 44.000 20.18 20.18 44.07 3.21
3172 6200 5.423015 AGCTAGTTACTGGAACATCACATG 58.577 41.667 5.41 0.00 40.86 3.21
3173 6201 5.683876 AGCTAGTTACTGGAACATCACAT 57.316 39.130 5.41 0.00 40.86 3.21
3174 6202 6.210784 ACTTAGCTAGTTACTGGAACATCACA 59.789 38.462 5.41 0.00 40.86 3.58
3175 6203 6.631962 ACTTAGCTAGTTACTGGAACATCAC 58.368 40.000 5.41 0.00 40.86 3.06
3176 6204 6.852420 ACTTAGCTAGTTACTGGAACATCA 57.148 37.500 5.41 0.00 40.86 3.07
3189 6217 9.683870 AGATGTAGTTGTAGTAACTTAGCTAGT 57.316 33.333 0.00 0.00 39.32 2.57
3191 6219 9.902684 AGAGATGTAGTTGTAGTAACTTAGCTA 57.097 33.333 0.00 0.00 0.00 3.32
3192 6220 8.810990 AGAGATGTAGTTGTAGTAACTTAGCT 57.189 34.615 0.00 0.00 0.00 3.32
3193 6221 8.130469 GGAGAGATGTAGTTGTAGTAACTTAGC 58.870 40.741 0.00 0.00 0.00 3.09
3194 6222 9.398538 AGGAGAGATGTAGTTGTAGTAACTTAG 57.601 37.037 0.00 0.00 0.00 2.18
3195 6223 9.393512 GAGGAGAGATGTAGTTGTAGTAACTTA 57.606 37.037 0.00 0.00 0.00 2.24
3196 6224 7.889073 TGAGGAGAGATGTAGTTGTAGTAACTT 59.111 37.037 0.00 0.00 0.00 2.66
3197 6225 7.403671 TGAGGAGAGATGTAGTTGTAGTAACT 58.596 38.462 0.00 0.00 0.00 2.24
3198 6226 7.627298 TGAGGAGAGATGTAGTTGTAGTAAC 57.373 40.000 0.00 0.00 0.00 2.50
3199 6227 8.824756 ATTGAGGAGAGATGTAGTTGTAGTAA 57.175 34.615 0.00 0.00 0.00 2.24
3200 6228 9.916360 TTATTGAGGAGAGATGTAGTTGTAGTA 57.084 33.333 0.00 0.00 0.00 1.82
3201 6229 8.688151 GTTATTGAGGAGAGATGTAGTTGTAGT 58.312 37.037 0.00 0.00 0.00 2.73
3202 6230 8.908903 AGTTATTGAGGAGAGATGTAGTTGTAG 58.091 37.037 0.00 0.00 0.00 2.74
3203 6231 8.824756 AGTTATTGAGGAGAGATGTAGTTGTA 57.175 34.615 0.00 0.00 0.00 2.41
3204 6232 7.397476 TGAGTTATTGAGGAGAGATGTAGTTGT 59.603 37.037 0.00 0.00 0.00 3.32
3205 6233 7.776107 TGAGTTATTGAGGAGAGATGTAGTTG 58.224 38.462 0.00 0.00 0.00 3.16
3206 6234 7.962995 TGAGTTATTGAGGAGAGATGTAGTT 57.037 36.000 0.00 0.00 0.00 2.24
3207 6235 8.546083 AATGAGTTATTGAGGAGAGATGTAGT 57.454 34.615 0.00 0.00 0.00 2.73
3221 6249 5.893687 TGCTTATGTGCCAATGAGTTATTG 58.106 37.500 0.67 0.67 44.67 1.90
3222 6250 6.528537 TTGCTTATGTGCCAATGAGTTATT 57.471 33.333 0.00 0.00 0.00 1.40
3223 6251 6.528537 TTTGCTTATGTGCCAATGAGTTAT 57.471 33.333 0.00 0.00 0.00 1.89
3224 6252 5.973899 TTTGCTTATGTGCCAATGAGTTA 57.026 34.783 0.00 0.00 0.00 2.24
3225 6253 4.870123 TTTGCTTATGTGCCAATGAGTT 57.130 36.364 0.00 0.00 0.00 3.01
3226 6254 5.410355 AATTTGCTTATGTGCCAATGAGT 57.590 34.783 0.00 0.00 30.32 3.41
3227 6255 6.102006 CAAATTTGCTTATGTGCCAATGAG 57.898 37.500 5.01 0.00 30.32 2.90
3242 6270 3.311966 GAGTCCAACTCAGCAAATTTGC 58.688 45.455 31.36 31.36 44.45 3.68
3243 6271 3.250762 TCGAGTCCAACTCAGCAAATTTG 59.749 43.478 14.03 14.03 45.30 2.32
3244 6272 3.476552 TCGAGTCCAACTCAGCAAATTT 58.523 40.909 7.78 0.00 45.30 1.82
3245 6273 3.126001 TCGAGTCCAACTCAGCAAATT 57.874 42.857 7.78 0.00 45.30 1.82
3246 6274 2.839486 TCGAGTCCAACTCAGCAAAT 57.161 45.000 7.78 0.00 45.30 2.32
3247 6275 2.224281 ACATCGAGTCCAACTCAGCAAA 60.224 45.455 7.78 0.00 45.30 3.68
3248 6276 1.344438 ACATCGAGTCCAACTCAGCAA 59.656 47.619 7.78 0.00 45.30 3.91
3249 6277 0.969149 ACATCGAGTCCAACTCAGCA 59.031 50.000 7.78 0.00 45.30 4.41
3250 6278 2.086054 AACATCGAGTCCAACTCAGC 57.914 50.000 7.78 0.00 45.30 4.26
3251 6279 4.169508 CAGTAACATCGAGTCCAACTCAG 58.830 47.826 7.78 1.37 45.30 3.35
3252 6280 3.614150 GCAGTAACATCGAGTCCAACTCA 60.614 47.826 7.78 0.00 45.30 3.41
3253 6281 2.924290 GCAGTAACATCGAGTCCAACTC 59.076 50.000 0.00 0.00 41.71 3.01
3254 6282 2.563179 AGCAGTAACATCGAGTCCAACT 59.437 45.455 0.00 0.00 0.00 3.16
3255 6283 2.668457 CAGCAGTAACATCGAGTCCAAC 59.332 50.000 0.00 0.00 0.00 3.77
3256 6284 2.560981 TCAGCAGTAACATCGAGTCCAA 59.439 45.455 0.00 0.00 0.00 3.53
3257 6285 2.167662 TCAGCAGTAACATCGAGTCCA 58.832 47.619 0.00 0.00 0.00 4.02
3258 6286 2.941453 TCAGCAGTAACATCGAGTCC 57.059 50.000 0.00 0.00 0.00 3.85
3259 6287 3.839293 ACTTCAGCAGTAACATCGAGTC 58.161 45.455 0.00 0.00 31.97 3.36
3260 6288 3.944055 ACTTCAGCAGTAACATCGAGT 57.056 42.857 0.00 0.00 31.97 4.18
3261 6289 5.403246 AGTAACTTCAGCAGTAACATCGAG 58.597 41.667 0.00 0.00 32.94 4.04
3262 6290 5.386958 AGTAACTTCAGCAGTAACATCGA 57.613 39.130 0.00 0.00 32.94 3.59
3263 6291 4.563184 GGAGTAACTTCAGCAGTAACATCG 59.437 45.833 0.00 0.00 32.94 3.84
3264 6292 4.870991 GGGAGTAACTTCAGCAGTAACATC 59.129 45.833 0.00 0.00 32.94 3.06
3265 6293 4.286032 TGGGAGTAACTTCAGCAGTAACAT 59.714 41.667 0.00 0.00 32.94 2.71
3266 6294 3.644265 TGGGAGTAACTTCAGCAGTAACA 59.356 43.478 0.00 0.00 32.94 2.41
3267 6295 4.267349 TGGGAGTAACTTCAGCAGTAAC 57.733 45.455 0.00 0.00 32.94 2.50
3268 6296 5.221843 ACAATGGGAGTAACTTCAGCAGTAA 60.222 40.000 0.00 0.00 32.94 2.24
3269 6297 4.286032 ACAATGGGAGTAACTTCAGCAGTA 59.714 41.667 0.00 0.00 32.94 2.74
3270 6298 3.073062 ACAATGGGAGTAACTTCAGCAGT 59.927 43.478 0.00 0.00 37.30 4.40
3271 6299 3.438087 CACAATGGGAGTAACTTCAGCAG 59.562 47.826 0.00 0.00 0.00 4.24
3272 6300 3.072330 TCACAATGGGAGTAACTTCAGCA 59.928 43.478 0.00 0.00 0.00 4.41
3273 6301 3.437049 GTCACAATGGGAGTAACTTCAGC 59.563 47.826 0.00 0.00 0.00 4.26
3274 6302 4.641396 TGTCACAATGGGAGTAACTTCAG 58.359 43.478 0.00 0.00 0.00 3.02
3275 6303 4.698201 TGTCACAATGGGAGTAACTTCA 57.302 40.909 0.00 0.00 0.00 3.02
3276 6304 5.049405 CACTTGTCACAATGGGAGTAACTTC 60.049 44.000 0.00 0.00 0.00 3.01
3277 6305 4.821805 CACTTGTCACAATGGGAGTAACTT 59.178 41.667 0.00 0.00 0.00 2.66
3278 6306 4.141482 ACACTTGTCACAATGGGAGTAACT 60.141 41.667 0.00 0.00 0.00 2.24
3279 6307 4.024048 CACACTTGTCACAATGGGAGTAAC 60.024 45.833 0.00 0.00 0.00 2.50
3280 6308 4.133820 CACACTTGTCACAATGGGAGTAA 58.866 43.478 0.00 0.00 0.00 2.24
3281 6309 3.389656 TCACACTTGTCACAATGGGAGTA 59.610 43.478 0.00 0.00 0.00 2.59
3282 6310 2.172505 TCACACTTGTCACAATGGGAGT 59.827 45.455 0.00 0.00 0.00 3.85
3283 6311 2.849942 TCACACTTGTCACAATGGGAG 58.150 47.619 0.00 0.00 0.00 4.30
3284 6312 3.289407 TTCACACTTGTCACAATGGGA 57.711 42.857 0.00 0.00 0.00 4.37
3285 6313 3.318839 ACATTCACACTTGTCACAATGGG 59.681 43.478 0.00 0.00 0.00 4.00
3286 6314 4.036616 TCACATTCACACTTGTCACAATGG 59.963 41.667 0.00 0.00 0.00 3.16
3287 6315 5.172460 TCACATTCACACTTGTCACAATG 57.828 39.130 0.00 0.00 0.00 2.82
3288 6316 4.276678 CCTCACATTCACACTTGTCACAAT 59.723 41.667 0.00 0.00 0.00 2.71
3289 6317 3.627123 CCTCACATTCACACTTGTCACAA 59.373 43.478 0.00 0.00 0.00 3.33
3290 6318 3.205338 CCTCACATTCACACTTGTCACA 58.795 45.455 0.00 0.00 0.00 3.58
3291 6319 2.549754 CCCTCACATTCACACTTGTCAC 59.450 50.000 0.00 0.00 0.00 3.67
3292 6320 2.172505 ACCCTCACATTCACACTTGTCA 59.827 45.455 0.00 0.00 0.00 3.58
3293 6321 2.549754 CACCCTCACATTCACACTTGTC 59.450 50.000 0.00 0.00 0.00 3.18
3294 6322 2.575532 CACCCTCACATTCACACTTGT 58.424 47.619 0.00 0.00 0.00 3.16
3295 6323 1.881973 CCACCCTCACATTCACACTTG 59.118 52.381 0.00 0.00 0.00 3.16
3296 6324 1.774254 TCCACCCTCACATTCACACTT 59.226 47.619 0.00 0.00 0.00 3.16
3297 6325 1.434188 TCCACCCTCACATTCACACT 58.566 50.000 0.00 0.00 0.00 3.55
3298 6326 2.270352 TTCCACCCTCACATTCACAC 57.730 50.000 0.00 0.00 0.00 3.82
3299 6327 3.304911 TTTTCCACCCTCACATTCACA 57.695 42.857 0.00 0.00 0.00 3.58
3349 6377 3.507162 ATTATGAATCGGCCATGTGGA 57.493 42.857 2.24 0.00 37.39 4.02
3445 6473 0.094730 GCAAGGTGCGTATCGTGTTC 59.905 55.000 1.42 0.00 31.71 3.18
3549 6583 3.846335 GCTACACGATTTTGTTTAGCAGC 59.154 43.478 10.04 0.00 43.97 5.25


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

AutoCloner maintained by Alex Coulton.