Multiple sequence alignment - TraesCS4D01G148100

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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 TraesCS4D01G148100 chr4D 100.000 2569 0 0 1 2569 145380595 145378027 0.000000e+00 4745.0
1 TraesCS4D01G148100 chr4D 90.335 1045 86 11 697 1734 348041026 348039990 0.000000e+00 1356.0
2 TraesCS4D01G148100 chr4D 91.130 699 60 2 3 700 459190647 459191344 0.000000e+00 946.0
3 TraesCS4D01G148100 chr5D 98.870 1328 14 1 697 2024 538687313 538688639 0.000000e+00 2368.0
4 TraesCS4D01G148100 chr5D 98.020 707 14 0 1 707 538686025 538686731 0.000000e+00 1229.0
5 TraesCS4D01G148100 chr5D 90.909 462 42 0 2070 2531 26447465 26447004 2.810000e-174 621.0
6 TraesCS4D01G148100 chr4A 95.724 1333 52 4 693 2023 629935808 629937137 0.000000e+00 2141.0
7 TraesCS4D01G148100 chr4A 97.647 680 15 1 1 680 629925590 629926268 0.000000e+00 1166.0
8 TraesCS4D01G148100 chr4A 95.349 43 1 1 2024 2065 342506457 342506499 1.650000e-07 67.6
9 TraesCS4D01G148100 chr1D 98.582 1128 16 0 895 2022 80683840 80684967 0.000000e+00 1995.0
10 TraesCS4D01G148100 chr1D 97.878 707 15 0 1 707 80673564 80674270 0.000000e+00 1223.0
11 TraesCS4D01G148100 chr1A 93.713 1336 53 16 693 2028 80283613 80282309 0.000000e+00 1973.0
12 TraesCS4D01G148100 chr1A 93.643 409 26 0 1616 2024 467752960 467753368 1.690000e-171 612.0
13 TraesCS4D01G148100 chr3D 89.941 1352 105 20 697 2029 339817345 339818684 0.000000e+00 1714.0
14 TraesCS4D01G148100 chr3D 94.067 691 40 1 10 700 339816084 339816773 0.000000e+00 1048.0
15 TraesCS4D01G148100 chr3D 91.361 463 40 0 2069 2531 420481893 420481431 3.610000e-178 634.0
16 TraesCS4D01G148100 chr2B 94.509 1038 53 3 697 1733 54562597 54561563 0.000000e+00 1598.0
17 TraesCS4D01G148100 chr2D 96.686 875 28 1 945 1818 27769206 27768332 0.000000e+00 1454.0
18 TraesCS4D01G148100 chr2D 91.013 701 59 3 3 700 469108632 469107933 0.000000e+00 942.0
19 TraesCS4D01G148100 chr2D 92.208 462 36 0 2070 2531 86856887 86857348 0.000000e+00 654.0
20 TraesCS4D01G148100 chr2D 90.638 470 40 3 2062 2531 86864825 86865290 2.810000e-174 621.0
21 TraesCS4D01G148100 chr7A 90.716 1034 84 10 702 1730 297775890 297774864 0.000000e+00 1367.0
22 TraesCS4D01G148100 chr7A 97.857 700 15 0 1 700 62735081 62735780 0.000000e+00 1210.0
23 TraesCS4D01G148100 chr7A 92.883 281 14 3 1750 2029 211154279 211154554 1.110000e-108 403.0
24 TraesCS4D01G148100 chr7D 97.000 700 21 0 1 700 78507739 78508438 0.000000e+00 1177.0
25 TraesCS4D01G148100 chr7D 91.489 470 38 2 2062 2531 347859149 347859616 0.000000e+00 645.0
26 TraesCS4D01G148100 chr7D 90.929 463 42 0 2069 2531 160903429 160902967 7.810000e-175 623.0
27 TraesCS4D01G148100 chr7D 90.570 456 43 0 2069 2524 357306071 357305616 2.830000e-169 604.0
28 TraesCS4D01G148100 chr7D 90.065 463 46 0 2069 2531 160895155 160894693 3.660000e-168 601.0
29 TraesCS4D01G148100 chr7D 90.351 456 44 0 2069 2524 357314147 357313692 1.320000e-167 599.0
30 TraesCS4D01G148100 chr5A 96.429 700 23 2 1 699 78448305 78449003 0.000000e+00 1153.0
31 TraesCS4D01G148100 chr5A 90.086 464 31 7 1576 2024 78449838 78450301 2.850000e-164 588.0
32 TraesCS4D01G148100 chr4B 93.597 734 33 8 1308 2029 413506962 413506231 0.000000e+00 1083.0
33 TraesCS4D01G148100 chr2A 83.539 972 132 11 707 1661 57826647 57827607 0.000000e+00 883.0
34 TraesCS4D01G148100 chrUn 88.674 362 26 5 1681 2027 47391621 47391982 6.570000e-116 427.0
35 TraesCS4D01G148100 chrUn 88.398 362 27 5 1681 2027 240783800 240783439 3.060000e-114 422.0
36 TraesCS4D01G148100 chr7B 94.444 36 2 0 1668 1703 551483129 551483094 3.570000e-04 56.5


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 TraesCS4D01G148100 chr4D 145378027 145380595 2568 True 4745.0 4745 100.0000 1 2569 1 chr4D.!!$R1 2568
1 TraesCS4D01G148100 chr4D 348039990 348041026 1036 True 1356.0 1356 90.3350 697 1734 1 chr4D.!!$R2 1037
2 TraesCS4D01G148100 chr4D 459190647 459191344 697 False 946.0 946 91.1300 3 700 1 chr4D.!!$F1 697
3 TraesCS4D01G148100 chr5D 538686025 538688639 2614 False 1798.5 2368 98.4450 1 2024 2 chr5D.!!$F1 2023
4 TraesCS4D01G148100 chr4A 629935808 629937137 1329 False 2141.0 2141 95.7240 693 2023 1 chr4A.!!$F3 1330
5 TraesCS4D01G148100 chr4A 629925590 629926268 678 False 1166.0 1166 97.6470 1 680 1 chr4A.!!$F2 679
6 TraesCS4D01G148100 chr1D 80683840 80684967 1127 False 1995.0 1995 98.5820 895 2022 1 chr1D.!!$F2 1127
7 TraesCS4D01G148100 chr1D 80673564 80674270 706 False 1223.0 1223 97.8780 1 707 1 chr1D.!!$F1 706
8 TraesCS4D01G148100 chr1A 80282309 80283613 1304 True 1973.0 1973 93.7130 693 2028 1 chr1A.!!$R1 1335
9 TraesCS4D01G148100 chr3D 339816084 339818684 2600 False 1381.0 1714 92.0040 10 2029 2 chr3D.!!$F1 2019
10 TraesCS4D01G148100 chr2B 54561563 54562597 1034 True 1598.0 1598 94.5090 697 1733 1 chr2B.!!$R1 1036
11 TraesCS4D01G148100 chr2D 27768332 27769206 874 True 1454.0 1454 96.6860 945 1818 1 chr2D.!!$R1 873
12 TraesCS4D01G148100 chr2D 469107933 469108632 699 True 942.0 942 91.0130 3 700 1 chr2D.!!$R2 697
13 TraesCS4D01G148100 chr7A 297774864 297775890 1026 True 1367.0 1367 90.7160 702 1730 1 chr7A.!!$R1 1028
14 TraesCS4D01G148100 chr7A 62735081 62735780 699 False 1210.0 1210 97.8570 1 700 1 chr7A.!!$F1 699
15 TraesCS4D01G148100 chr7D 78507739 78508438 699 False 1177.0 1177 97.0000 1 700 1 chr7D.!!$F1 699
16 TraesCS4D01G148100 chr5A 78448305 78450301 1996 False 870.5 1153 93.2575 1 2024 2 chr5A.!!$F1 2023
17 TraesCS4D01G148100 chr4B 413506231 413506962 731 True 1083.0 1083 93.5970 1308 2029 1 chr4B.!!$R1 721
18 TraesCS4D01G148100 chr2A 57826647 57827607 960 False 883.0 883 83.5390 707 1661 1 chr2A.!!$F1 954

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
40 41 1.208293 TCATACGGCACAACCAGCATA 59.792 47.619 0.0 0.0 39.03 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2769 0.896226 CCTAGGGTTAGATAGGCGGC 59.104 60.0 0.0 0.0 32.6 6.53 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
40 41 1.208293 TCATACGGCACAACCAGCATA 59.792 47.619 0.00 0.00 39.03 3.14
298 299 5.279106 CCAAAGATGTGGAGCATTCTTTTCA 60.279 40.000 0.00 0.00 41.65 2.69
378 379 3.173668 TCACGTATGTATTGGCTGGTC 57.826 47.619 0.00 0.00 0.00 4.02
685 689 4.777896 TCAACCTTAGGCACTCTTCACTAT 59.222 41.667 0.00 0.00 41.75 2.12
744 1421 2.890311 TCCATGACGAAAACCATGCTTT 59.110 40.909 0.00 0.00 38.95 3.51
746 1423 3.552684 CCATGACGAAAACCATGCTTTGT 60.553 43.478 0.00 0.00 38.95 2.83
1016 1699 4.319046 GCATTGTATGGTATGCTTCTCACG 60.319 45.833 0.00 0.00 42.91 4.35
1215 1903 8.056407 TCTTCTTTCTATTGATCTCGAAGACA 57.944 34.615 0.00 0.00 33.00 3.41
1375 2076 0.308993 GCTGAAGCGCTTGTGAAGTT 59.691 50.000 30.47 0.00 0.00 2.66
1590 2291 9.621629 TCTAAATTCGATATGGTTGTATGGTTT 57.378 29.630 0.00 0.00 0.00 3.27
1618 2320 6.946340 AGTATGTGAACTTGACATGTATGGA 58.054 36.000 0.00 0.00 35.62 3.41
2024 2760 2.137528 CCCCAACCAAACACACCCC 61.138 63.158 0.00 0.00 0.00 4.95
2028 2764 1.960689 CCAACCAAACACACCCCTAAG 59.039 52.381 0.00 0.00 0.00 2.18
2029 2765 1.339929 CAACCAAACACACCCCTAAGC 59.660 52.381 0.00 0.00 0.00 3.09
2030 2766 0.178973 ACCAAACACACCCCTAAGCC 60.179 55.000 0.00 0.00 0.00 4.35
2031 2767 0.898326 CCAAACACACCCCTAAGCCC 60.898 60.000 0.00 0.00 0.00 5.19
2032 2768 0.178975 CAAACACACCCCTAAGCCCA 60.179 55.000 0.00 0.00 0.00 5.36
2033 2769 0.112412 AAACACACCCCTAAGCCCAG 59.888 55.000 0.00 0.00 0.00 4.45
2034 2770 2.044946 CACACCCCTAAGCCCAGC 60.045 66.667 0.00 0.00 0.00 4.85
2035 2771 3.339093 ACACCCCTAAGCCCAGCC 61.339 66.667 0.00 0.00 0.00 4.85
2036 2772 4.489771 CACCCCTAAGCCCAGCCG 62.490 72.222 0.00 0.00 0.00 5.52
2040 2776 3.161450 CCTAAGCCCAGCCGCCTA 61.161 66.667 0.00 0.00 0.00 3.93
2041 2777 2.520536 CCTAAGCCCAGCCGCCTAT 61.521 63.158 0.00 0.00 0.00 2.57
2042 2778 1.004440 CTAAGCCCAGCCGCCTATC 60.004 63.158 0.00 0.00 0.00 2.08
2043 2779 1.459539 TAAGCCCAGCCGCCTATCT 60.460 57.895 0.00 0.00 0.00 1.98
2044 2780 0.178944 TAAGCCCAGCCGCCTATCTA 60.179 55.000 0.00 0.00 0.00 1.98
2045 2781 1.054406 AAGCCCAGCCGCCTATCTAA 61.054 55.000 0.00 0.00 0.00 2.10
2046 2782 1.301795 GCCCAGCCGCCTATCTAAC 60.302 63.158 0.00 0.00 0.00 2.34
2047 2783 1.371558 CCCAGCCGCCTATCTAACC 59.628 63.158 0.00 0.00 0.00 2.85
2048 2784 1.371558 CCAGCCGCCTATCTAACCC 59.628 63.158 0.00 0.00 0.00 4.11
2049 2785 1.122019 CCAGCCGCCTATCTAACCCT 61.122 60.000 0.00 0.00 0.00 4.34
2050 2786 1.629043 CAGCCGCCTATCTAACCCTA 58.371 55.000 0.00 0.00 0.00 3.53
2051 2787 1.546476 CAGCCGCCTATCTAACCCTAG 59.454 57.143 0.00 0.00 0.00 3.02
2052 2788 0.896226 GCCGCCTATCTAACCCTAGG 59.104 60.000 0.06 0.06 38.03 3.02
2053 2789 1.826442 GCCGCCTATCTAACCCTAGGT 60.826 57.143 8.29 0.00 37.43 3.08
2054 2790 2.169330 CCGCCTATCTAACCCTAGGTC 58.831 57.143 8.29 0.00 37.43 3.85
2055 2791 2.169330 CGCCTATCTAACCCTAGGTCC 58.831 57.143 8.29 0.00 37.43 4.46
2056 2792 2.169330 GCCTATCTAACCCTAGGTCCG 58.831 57.143 8.29 0.00 37.43 4.79
2057 2793 2.224967 GCCTATCTAACCCTAGGTCCGA 60.225 54.545 8.29 0.00 37.43 4.55
2058 2794 3.419943 CCTATCTAACCCTAGGTCCGAC 58.580 54.545 8.29 0.00 33.12 4.79
2059 2795 2.378378 ATCTAACCCTAGGTCCGACC 57.622 55.000 9.81 9.81 38.99 4.79
2060 2796 0.259938 TCTAACCCTAGGTCCGACCC 59.740 60.000 14.32 0.00 39.75 4.46
2061 2797 0.758310 CTAACCCTAGGTCCGACCCC 60.758 65.000 14.32 0.00 39.75 4.95
2062 2798 2.242408 TAACCCTAGGTCCGACCCCC 62.242 65.000 14.32 0.00 39.75 5.40
2063 2799 3.763757 CCCTAGGTCCGACCCCCT 61.764 72.222 14.32 0.00 39.75 4.79
2064 2800 2.123382 CCTAGGTCCGACCCCCTC 60.123 72.222 14.32 0.00 39.75 4.30
2065 2801 2.518825 CTAGGTCCGACCCCCTCG 60.519 72.222 14.32 0.00 39.75 4.63
2066 2802 4.828296 TAGGTCCGACCCCCTCGC 62.828 72.222 14.32 0.00 39.75 5.03
2070 2806 4.377760 TCCGACCCCCTCGCTCTT 62.378 66.667 0.00 0.00 41.46 2.85
2071 2807 3.839432 CCGACCCCCTCGCTCTTC 61.839 72.222 0.00 0.00 41.46 2.87
2072 2808 2.756283 CGACCCCCTCGCTCTTCT 60.756 66.667 0.00 0.00 35.06 2.85
2073 2809 2.776913 CGACCCCCTCGCTCTTCTC 61.777 68.421 0.00 0.00 35.06 2.87
2074 2810 1.380650 GACCCCCTCGCTCTTCTCT 60.381 63.158 0.00 0.00 0.00 3.10
2075 2811 1.380650 ACCCCCTCGCTCTTCTCTC 60.381 63.158 0.00 0.00 0.00 3.20
2076 2812 2.485795 CCCCCTCGCTCTTCTCTCG 61.486 68.421 0.00 0.00 0.00 4.04
2077 2813 1.452289 CCCCTCGCTCTTCTCTCGA 60.452 63.158 0.00 0.00 0.00 4.04
2078 2814 0.821711 CCCCTCGCTCTTCTCTCGAT 60.822 60.000 0.00 0.00 0.00 3.59
2079 2815 0.591170 CCCTCGCTCTTCTCTCGATC 59.409 60.000 0.00 0.00 0.00 3.69
2080 2816 0.591170 CCTCGCTCTTCTCTCGATCC 59.409 60.000 0.00 0.00 0.00 3.36
2081 2817 0.591170 CTCGCTCTTCTCTCGATCCC 59.409 60.000 0.00 0.00 0.00 3.85
2082 2818 0.107165 TCGCTCTTCTCTCGATCCCA 60.107 55.000 0.00 0.00 0.00 4.37
2083 2819 0.958091 CGCTCTTCTCTCGATCCCAT 59.042 55.000 0.00 0.00 0.00 4.00
2084 2820 1.068610 CGCTCTTCTCTCGATCCCATC 60.069 57.143 0.00 0.00 0.00 3.51
2085 2821 2.238521 GCTCTTCTCTCGATCCCATCT 58.761 52.381 0.00 0.00 0.00 2.90
2086 2822 2.228822 GCTCTTCTCTCGATCCCATCTC 59.771 54.545 0.00 0.00 0.00 2.75
2087 2823 2.819608 CTCTTCTCTCGATCCCATCTCC 59.180 54.545 0.00 0.00 0.00 3.71
2088 2824 1.892474 CTTCTCTCGATCCCATCTCCC 59.108 57.143 0.00 0.00 0.00 4.30
2089 2825 1.153539 TCTCTCGATCCCATCTCCCT 58.846 55.000 0.00 0.00 0.00 4.20
2090 2826 1.074727 TCTCTCGATCCCATCTCCCTC 59.925 57.143 0.00 0.00 0.00 4.30
2091 2827 0.113385 TCTCGATCCCATCTCCCTCC 59.887 60.000 0.00 0.00 0.00 4.30
2092 2828 0.178950 CTCGATCCCATCTCCCTCCA 60.179 60.000 0.00 0.00 0.00 3.86
2093 2829 0.178950 TCGATCCCATCTCCCTCCAG 60.179 60.000 0.00 0.00 0.00 3.86
2094 2830 1.825281 CGATCCCATCTCCCTCCAGC 61.825 65.000 0.00 0.00 0.00 4.85
2095 2831 1.825281 GATCCCATCTCCCTCCAGCG 61.825 65.000 0.00 0.00 0.00 5.18
2096 2832 4.247380 CCCATCTCCCTCCAGCGC 62.247 72.222 0.00 0.00 0.00 5.92
2097 2833 4.247380 CCATCTCCCTCCAGCGCC 62.247 72.222 2.29 0.00 0.00 6.53
2098 2834 4.598894 CATCTCCCTCCAGCGCCG 62.599 72.222 2.29 0.00 0.00 6.46
2111 2847 3.849951 CGCCGCCAGTACCCTGAT 61.850 66.667 0.00 0.00 41.50 2.90
2112 2848 2.109181 GCCGCCAGTACCCTGATC 59.891 66.667 0.00 0.00 41.50 2.92
2113 2849 2.822399 CCGCCAGTACCCTGATCC 59.178 66.667 0.00 0.00 41.50 3.36
2114 2850 2.808206 CCGCCAGTACCCTGATCCC 61.808 68.421 0.00 0.00 41.50 3.85
2115 2851 2.808206 CGCCAGTACCCTGATCCCC 61.808 68.421 0.00 0.00 41.50 4.81
2116 2852 1.692749 GCCAGTACCCTGATCCCCA 60.693 63.158 0.00 0.00 41.50 4.96
2117 2853 1.062488 GCCAGTACCCTGATCCCCAT 61.062 60.000 0.00 0.00 41.50 4.00
2118 2854 1.059913 CCAGTACCCTGATCCCCATC 58.940 60.000 0.00 0.00 41.50 3.51
2119 2855 1.415126 CCAGTACCCTGATCCCCATCT 60.415 57.143 0.00 0.00 41.50 2.90
2120 2856 1.974236 CAGTACCCTGATCCCCATCTC 59.026 57.143 0.00 0.00 41.50 2.75
2121 2857 1.132689 AGTACCCTGATCCCCATCTCC 60.133 57.143 0.00 0.00 0.00 3.71
2122 2858 0.193574 TACCCTGATCCCCATCTCCC 59.806 60.000 0.00 0.00 0.00 4.30
2123 2859 1.241327 CCCTGATCCCCATCTCCCT 59.759 63.158 0.00 0.00 0.00 4.20
2124 2860 0.839853 CCCTGATCCCCATCTCCCTC 60.840 65.000 0.00 0.00 0.00 4.30
2125 2861 0.839853 CCTGATCCCCATCTCCCTCC 60.840 65.000 0.00 0.00 0.00 4.30
2126 2862 1.152247 TGATCCCCATCTCCCTCCG 60.152 63.158 0.00 0.00 0.00 4.63
2127 2863 2.527875 ATCCCCATCTCCCTCCGC 60.528 66.667 0.00 0.00 0.00 5.54
2128 2864 3.106859 ATCCCCATCTCCCTCCGCT 62.107 63.158 0.00 0.00 0.00 5.52
2129 2865 3.237741 CCCCATCTCCCTCCGCTC 61.238 72.222 0.00 0.00 0.00 5.03
2130 2866 3.610669 CCCATCTCCCTCCGCTCG 61.611 72.222 0.00 0.00 0.00 5.03
2131 2867 2.519541 CCATCTCCCTCCGCTCGA 60.520 66.667 0.00 0.00 0.00 4.04
2132 2868 1.905843 CCATCTCCCTCCGCTCGAT 60.906 63.158 0.00 0.00 0.00 3.59
2133 2869 1.583986 CATCTCCCTCCGCTCGATC 59.416 63.158 0.00 0.00 0.00 3.69
2134 2870 0.893270 CATCTCCCTCCGCTCGATCT 60.893 60.000 0.00 0.00 0.00 2.75
2135 2871 0.608035 ATCTCCCTCCGCTCGATCTC 60.608 60.000 0.00 0.00 0.00 2.75
2136 2872 2.203365 TCCCTCCGCTCGATCTCC 60.203 66.667 0.00 0.00 0.00 3.71
2137 2873 2.203422 CCCTCCGCTCGATCTCCT 60.203 66.667 0.00 0.00 0.00 3.69
2138 2874 2.265182 CCCTCCGCTCGATCTCCTC 61.265 68.421 0.00 0.00 0.00 3.71
2139 2875 2.265182 CCTCCGCTCGATCTCCTCC 61.265 68.421 0.00 0.00 0.00 4.30
2140 2876 1.228124 CTCCGCTCGATCTCCTCCT 60.228 63.158 0.00 0.00 0.00 3.69
2141 2877 1.228003 TCCGCTCGATCTCCTCCTC 60.228 63.158 0.00 0.00 0.00 3.71
2142 2878 1.527148 CCGCTCGATCTCCTCCTCA 60.527 63.158 0.00 0.00 0.00 3.86
2143 2879 1.514678 CCGCTCGATCTCCTCCTCAG 61.515 65.000 0.00 0.00 0.00 3.35
2144 2880 1.659794 GCTCGATCTCCTCCTCAGC 59.340 63.158 0.00 0.00 0.00 4.26
2145 2881 1.805428 GCTCGATCTCCTCCTCAGCC 61.805 65.000 0.00 0.00 0.00 4.85
2146 2882 0.178992 CTCGATCTCCTCCTCAGCCT 60.179 60.000 0.00 0.00 0.00 4.58
2147 2883 0.179004 TCGATCTCCTCCTCAGCCTC 60.179 60.000 0.00 0.00 0.00 4.70
2148 2884 0.178992 CGATCTCCTCCTCAGCCTCT 60.179 60.000 0.00 0.00 0.00 3.69
2149 2885 1.620822 GATCTCCTCCTCAGCCTCTC 58.379 60.000 0.00 0.00 0.00 3.20
2150 2886 0.178992 ATCTCCTCCTCAGCCTCTCG 60.179 60.000 0.00 0.00 0.00 4.04
2151 2887 1.225983 CTCCTCCTCAGCCTCTCGA 59.774 63.158 0.00 0.00 0.00 4.04
2152 2888 0.178992 CTCCTCCTCAGCCTCTCGAT 60.179 60.000 0.00 0.00 0.00 3.59
2153 2889 0.179004 TCCTCCTCAGCCTCTCGATC 60.179 60.000 0.00 0.00 0.00 3.69
2154 2890 0.178992 CCTCCTCAGCCTCTCGATCT 60.179 60.000 0.00 0.00 0.00 2.75
2155 2891 1.238439 CTCCTCAGCCTCTCGATCTC 58.762 60.000 0.00 0.00 0.00 2.75
2156 2892 0.179004 TCCTCAGCCTCTCGATCTCC 60.179 60.000 0.00 0.00 0.00 3.71
2157 2893 1.178534 CCTCAGCCTCTCGATCTCCC 61.179 65.000 0.00 0.00 0.00 4.30
2158 2894 0.467106 CTCAGCCTCTCGATCTCCCA 60.467 60.000 0.00 0.00 0.00 4.37
2159 2895 0.753479 TCAGCCTCTCGATCTCCCAC 60.753 60.000 0.00 0.00 0.00 4.61
2160 2896 1.039785 CAGCCTCTCGATCTCCCACA 61.040 60.000 0.00 0.00 0.00 4.17
2161 2897 1.040339 AGCCTCTCGATCTCCCACAC 61.040 60.000 0.00 0.00 0.00 3.82
2162 2898 1.730487 CCTCTCGATCTCCCACACG 59.270 63.158 0.00 0.00 0.00 4.49
2163 2899 1.064946 CTCTCGATCTCCCACACGC 59.935 63.158 0.00 0.00 0.00 5.34
2164 2900 1.657751 CTCTCGATCTCCCACACGCA 61.658 60.000 0.00 0.00 0.00 5.24
2165 2901 1.037579 TCTCGATCTCCCACACGCAT 61.038 55.000 0.00 0.00 0.00 4.73
2166 2902 0.668535 CTCGATCTCCCACACGCATA 59.331 55.000 0.00 0.00 0.00 3.14
2167 2903 0.384309 TCGATCTCCCACACGCATAC 59.616 55.000 0.00 0.00 0.00 2.39
2168 2904 0.102300 CGATCTCCCACACGCATACA 59.898 55.000 0.00 0.00 0.00 2.29
2169 2905 1.571919 GATCTCCCACACGCATACAC 58.428 55.000 0.00 0.00 0.00 2.90
2170 2906 0.178068 ATCTCCCACACGCATACACC 59.822 55.000 0.00 0.00 0.00 4.16
2171 2907 1.449601 CTCCCACACGCATACACCC 60.450 63.158 0.00 0.00 0.00 4.61
2172 2908 2.178876 CTCCCACACGCATACACCCA 62.179 60.000 0.00 0.00 0.00 4.51
2173 2909 1.745115 CCCACACGCATACACCCAG 60.745 63.158 0.00 0.00 0.00 4.45
2174 2910 2.398554 CCACACGCATACACCCAGC 61.399 63.158 0.00 0.00 0.00 4.85
2178 2914 4.838152 CGCATACACCCAGCGCCT 62.838 66.667 2.29 0.00 45.14 5.52
2179 2915 2.897350 GCATACACCCAGCGCCTC 60.897 66.667 2.29 0.00 0.00 4.70
2180 2916 2.203070 CATACACCCAGCGCCTCC 60.203 66.667 2.29 0.00 0.00 4.30
2181 2917 2.687200 ATACACCCAGCGCCTCCA 60.687 61.111 2.29 0.00 0.00 3.86
2182 2918 2.297895 ATACACCCAGCGCCTCCAA 61.298 57.895 2.29 0.00 0.00 3.53
2183 2919 2.257409 ATACACCCAGCGCCTCCAAG 62.257 60.000 2.29 0.00 0.00 3.61
2202 2938 3.607661 GAGACGCCCGATCCCCTC 61.608 72.222 0.00 0.00 0.00 4.30
2211 2947 2.413765 GATCCCCTCGACGCTGAC 59.586 66.667 0.00 0.00 0.00 3.51
2212 2948 3.140225 GATCCCCTCGACGCTGACC 62.140 68.421 0.00 0.00 0.00 4.02
2213 2949 3.663815 ATCCCCTCGACGCTGACCT 62.664 63.158 0.00 0.00 0.00 3.85
2214 2950 3.827898 CCCCTCGACGCTGACCTC 61.828 72.222 0.00 0.00 0.00 3.85
2215 2951 4.180946 CCCTCGACGCTGACCTCG 62.181 72.222 0.00 0.00 0.00 4.63
2216 2952 4.180946 CCTCGACGCTGACCTCGG 62.181 72.222 0.00 0.00 0.00 4.63
2217 2953 4.838486 CTCGACGCTGACCTCGGC 62.838 72.222 0.00 0.00 44.53 5.54
2224 2960 2.892425 CTGACCTCGGCATTCGGC 60.892 66.667 0.00 0.00 43.74 5.54
2254 2990 4.742201 CCGACGACCACCAGCAGG 62.742 72.222 0.00 0.00 42.21 4.85
2255 2991 4.742201 CGACGACCACCAGCAGGG 62.742 72.222 0.00 0.00 44.81 4.45
2293 3029 4.821589 CACGCCGGCCTCTCCTTC 62.822 72.222 23.46 0.00 0.00 3.46
2296 3032 3.855853 GCCGGCCTCTCCTTCCTC 61.856 72.222 18.11 0.00 0.00 3.71
2297 3033 3.157949 CCGGCCTCTCCTTCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
2298 3034 3.532155 CGGCCTCTCCTTCCTCCG 61.532 72.222 0.00 0.00 0.00 4.63
2299 3035 3.855853 GGCCTCTCCTTCCTCCGC 61.856 72.222 0.00 0.00 0.00 5.54
2300 3036 3.855853 GCCTCTCCTTCCTCCGCC 61.856 72.222 0.00 0.00 0.00 6.13
2301 3037 3.157949 CCTCTCCTTCCTCCGCCC 61.158 72.222 0.00 0.00 0.00 6.13
2302 3038 2.364317 CTCTCCTTCCTCCGCCCA 60.364 66.667 0.00 0.00 0.00 5.36
2303 3039 1.990060 CTCTCCTTCCTCCGCCCAA 60.990 63.158 0.00 0.00 0.00 4.12
2304 3040 2.245438 CTCTCCTTCCTCCGCCCAAC 62.245 65.000 0.00 0.00 0.00 3.77
2305 3041 3.327404 TCCTTCCTCCGCCCAACC 61.327 66.667 0.00 0.00 0.00 3.77
2306 3042 3.330720 CCTTCCTCCGCCCAACCT 61.331 66.667 0.00 0.00 0.00 3.50
2307 3043 2.269241 CTTCCTCCGCCCAACCTC 59.731 66.667 0.00 0.00 0.00 3.85
2308 3044 2.528127 TTCCTCCGCCCAACCTCA 60.528 61.111 0.00 0.00 0.00 3.86
2309 3045 2.527951 CTTCCTCCGCCCAACCTCAG 62.528 65.000 0.00 0.00 0.00 3.35
2310 3046 4.785453 CCTCCGCCCAACCTCAGC 62.785 72.222 0.00 0.00 0.00 4.26
2311 3047 4.785453 CTCCGCCCAACCTCAGCC 62.785 72.222 0.00 0.00 0.00 4.85
2313 3049 4.431131 CCGCCCAACCTCAGCCAT 62.431 66.667 0.00 0.00 0.00 4.40
2314 3050 3.136123 CGCCCAACCTCAGCCATG 61.136 66.667 0.00 0.00 0.00 3.66
2315 3051 2.757099 GCCCAACCTCAGCCATGG 60.757 66.667 7.63 7.63 0.00 3.66
2316 3052 3.089838 CCCAACCTCAGCCATGGA 58.910 61.111 18.40 0.00 34.82 3.41
2317 3053 1.379044 CCCAACCTCAGCCATGGAC 60.379 63.158 18.40 7.03 34.82 4.02
2318 3054 1.746615 CCAACCTCAGCCATGGACG 60.747 63.158 18.40 5.03 34.82 4.79
2319 3055 1.003355 CAACCTCAGCCATGGACGT 60.003 57.895 18.40 0.00 0.00 4.34
2320 3056 1.003355 AACCTCAGCCATGGACGTG 60.003 57.895 18.40 9.46 0.00 4.49
2321 3057 2.821366 CCTCAGCCATGGACGTGC 60.821 66.667 18.40 0.00 0.00 5.34
2322 3058 2.046988 CTCAGCCATGGACGTGCA 60.047 61.111 18.40 13.59 0.00 4.57
2323 3059 2.358615 TCAGCCATGGACGTGCAC 60.359 61.111 18.40 6.82 0.00 4.57
2324 3060 2.359107 CAGCCATGGACGTGCACT 60.359 61.111 18.40 1.71 0.00 4.40
2325 3061 2.359107 AGCCATGGACGTGCACTG 60.359 61.111 18.40 11.79 0.00 3.66
2326 3062 4.107051 GCCATGGACGTGCACTGC 62.107 66.667 18.40 14.45 0.00 4.40
2327 3063 3.434319 CCATGGACGTGCACTGCC 61.434 66.667 13.47 15.84 0.00 4.85
2328 3064 3.792047 CATGGACGTGCACTGCCG 61.792 66.667 13.47 3.81 0.00 5.69
2331 3067 4.735132 GGACGTGCACTGCCGCTA 62.735 66.667 16.19 0.00 0.00 4.26
2332 3068 3.479269 GACGTGCACTGCCGCTAC 61.479 66.667 16.19 0.00 0.00 3.58
2333 3069 3.916392 GACGTGCACTGCCGCTACT 62.916 63.158 16.19 0.00 0.00 2.57
2334 3070 3.181967 CGTGCACTGCCGCTACTC 61.182 66.667 16.19 0.00 0.00 2.59
2335 3071 2.262915 GTGCACTGCCGCTACTCT 59.737 61.111 10.32 0.00 0.00 3.24
2336 3072 2.097038 GTGCACTGCCGCTACTCTG 61.097 63.158 10.32 0.00 0.00 3.35
2337 3073 3.191539 GCACTGCCGCTACTCTGC 61.192 66.667 0.00 0.00 0.00 4.26
2338 3074 2.575993 CACTGCCGCTACTCTGCT 59.424 61.111 0.00 0.00 0.00 4.24
2339 3075 1.808799 CACTGCCGCTACTCTGCTG 60.809 63.158 0.00 0.00 0.00 4.41
2340 3076 2.889503 CTGCCGCTACTCTGCTGC 60.890 66.667 0.00 0.00 42.22 5.25
2341 3077 4.801624 TGCCGCTACTCTGCTGCG 62.802 66.667 0.00 0.00 44.26 5.18
2376 3112 3.423154 GTCACGCCCGCTCCTTTG 61.423 66.667 0.00 0.00 0.00 2.77
2382 3118 2.268920 CCCGCTCCTTTGCTGCTA 59.731 61.111 0.00 0.00 0.00 3.49
2383 3119 2.109126 CCCGCTCCTTTGCTGCTAC 61.109 63.158 0.00 0.00 0.00 3.58
2384 3120 2.109126 CCGCTCCTTTGCTGCTACC 61.109 63.158 0.00 0.00 0.00 3.18
2385 3121 2.109126 CGCTCCTTTGCTGCTACCC 61.109 63.158 0.00 0.00 0.00 3.69
2386 3122 2.109126 GCTCCTTTGCTGCTACCCG 61.109 63.158 0.00 0.00 0.00 5.28
2387 3123 1.450312 CTCCTTTGCTGCTACCCGG 60.450 63.158 0.00 0.00 0.00 5.73
2388 3124 1.899437 CTCCTTTGCTGCTACCCGGA 61.899 60.000 0.73 0.00 0.00 5.14
2389 3125 1.745489 CCTTTGCTGCTACCCGGAC 60.745 63.158 0.73 0.00 0.00 4.79
2390 3126 2.047655 TTTGCTGCTACCCGGACG 60.048 61.111 0.73 0.00 0.00 4.79
2391 3127 2.781595 CTTTGCTGCTACCCGGACGT 62.782 60.000 0.73 0.00 0.00 4.34
2392 3128 2.775032 TTTGCTGCTACCCGGACGTC 62.775 60.000 7.13 7.13 0.00 4.34
2393 3129 4.509737 GCTGCTACCCGGACGTCC 62.510 72.222 25.28 25.28 0.00 4.79
2394 3130 3.834799 CTGCTACCCGGACGTCCC 61.835 72.222 28.52 13.81 0.00 4.46
2395 3131 4.371417 TGCTACCCGGACGTCCCT 62.371 66.667 28.52 13.60 0.00 4.20
2396 3132 3.834799 GCTACCCGGACGTCCCTG 61.835 72.222 28.52 21.00 0.00 4.45
2397 3133 3.834799 CTACCCGGACGTCCCTGC 61.835 72.222 28.52 4.12 0.00 4.85
2416 3152 3.730761 GCCAAGTGCGCCAGAGTG 61.731 66.667 4.18 0.00 0.00 3.51
2445 3181 4.452733 CTGGTTCCCCGCCTCGTC 62.453 72.222 0.00 0.00 0.00 4.20
2474 3210 3.069318 GTCCCCGAGCTCCGAGTT 61.069 66.667 8.47 0.00 41.76 3.01
2475 3211 3.068691 TCCCCGAGCTCCGAGTTG 61.069 66.667 8.47 0.00 41.76 3.16
2476 3212 4.148825 CCCCGAGCTCCGAGTTGG 62.149 72.222 8.47 1.80 41.76 3.77
2477 3213 4.821589 CCCGAGCTCCGAGTTGGC 62.822 72.222 8.47 0.00 41.76 4.52
2478 3214 4.821589 CCGAGCTCCGAGTTGGCC 62.822 72.222 8.47 0.00 41.76 5.36
2517 3253 3.518998 CGTCCTCTCGCCGGTGAT 61.519 66.667 19.93 0.00 0.00 3.06
2518 3254 2.413765 GTCCTCTCGCCGGTGATC 59.586 66.667 19.93 3.55 0.00 2.92
2519 3255 2.044352 TCCTCTCGCCGGTGATCA 60.044 61.111 19.93 7.41 0.00 2.92
2520 3256 2.121538 TCCTCTCGCCGGTGATCAG 61.122 63.158 19.93 16.67 0.00 2.90
2521 3257 2.279120 CTCTCGCCGGTGATCAGC 60.279 66.667 19.93 15.01 0.00 4.26
2522 3258 3.068064 TCTCGCCGGTGATCAGCA 61.068 61.111 19.93 4.20 0.00 4.41
2523 3259 2.887568 CTCGCCGGTGATCAGCAC 60.888 66.667 19.93 14.12 46.98 4.40
2531 3267 2.938354 GTGATCAGCACAAGCAGGT 58.062 52.632 0.00 0.00 46.91 4.00
2532 3268 0.801251 GTGATCAGCACAAGCAGGTC 59.199 55.000 0.00 0.00 46.91 3.85
2533 3269 0.397564 TGATCAGCACAAGCAGGTCA 59.602 50.000 0.00 0.00 43.96 4.02
2534 3270 1.003928 TGATCAGCACAAGCAGGTCAT 59.996 47.619 0.00 0.00 41.72 3.06
2535 3271 1.669779 GATCAGCACAAGCAGGTCATC 59.330 52.381 0.00 0.00 45.49 2.92
2536 3272 0.321919 TCAGCACAAGCAGGTCATCC 60.322 55.000 0.00 0.00 45.49 3.51
2537 3273 0.322277 CAGCACAAGCAGGTCATCCT 60.322 55.000 0.00 0.00 46.37 3.24
2538 3274 0.035630 AGCACAAGCAGGTCATCCTC 60.036 55.000 0.00 0.00 43.07 3.71
2539 3275 1.364626 GCACAAGCAGGTCATCCTCG 61.365 60.000 0.00 0.00 43.07 4.63
2540 3276 1.078848 ACAAGCAGGTCATCCTCGC 60.079 57.895 0.00 0.00 43.07 5.03
2541 3277 1.817099 CAAGCAGGTCATCCTCGCC 60.817 63.158 0.00 0.00 43.07 5.54
2542 3278 3.376935 AAGCAGGTCATCCTCGCCG 62.377 63.158 0.00 0.00 43.07 6.46
2543 3279 4.148825 GCAGGTCATCCTCGCCGT 62.149 66.667 0.00 0.00 43.07 5.68
2544 3280 2.105128 CAGGTCATCCTCGCCGTC 59.895 66.667 0.00 0.00 43.07 4.79
2545 3281 3.518998 AGGTCATCCTCGCCGTCG 61.519 66.667 0.00 0.00 40.58 5.12
2558 3294 4.778415 CGTCGCCGTCACCAGGAG 62.778 72.222 0.00 0.00 0.00 3.69
2559 3295 4.436998 GTCGCCGTCACCAGGAGG 62.437 72.222 0.00 0.00 42.21 4.30
2560 3296 4.671590 TCGCCGTCACCAGGAGGA 62.672 66.667 0.00 0.00 38.69 3.71
2561 3297 4.135153 CGCCGTCACCAGGAGGAG 62.135 72.222 0.00 0.00 38.69 3.69
2562 3298 4.459089 GCCGTCACCAGGAGGAGC 62.459 72.222 0.00 0.00 38.69 4.70
2563 3299 2.681778 CCGTCACCAGGAGGAGCT 60.682 66.667 0.00 0.00 38.69 4.09
2564 3300 2.716017 CCGTCACCAGGAGGAGCTC 61.716 68.421 4.71 4.71 38.69 4.09
2565 3301 2.888863 GTCACCAGGAGGAGCTCG 59.111 66.667 7.83 0.00 38.69 5.03
2566 3302 1.979693 GTCACCAGGAGGAGCTCGT 60.980 63.158 9.04 9.04 38.69 4.18
2567 3303 1.679305 TCACCAGGAGGAGCTCGTC 60.679 63.158 24.90 24.90 38.69 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 8.593945 TGGCATGAAGAACCTTTCTAAAATAT 57.406 30.769 0.00 0.00 39.61 1.28
78 79 7.801104 TGATGGTGGCCGTATATAATCATTAT 58.199 34.615 0.00 0.00 0.00 1.28
298 299 3.591977 AGTTGTAAAGGCCTTCCTACCAT 59.408 43.478 20.79 3.26 43.40 3.55
378 379 2.358737 GTGTGCTGACCCTTCCCG 60.359 66.667 0.00 0.00 0.00 5.14
462 463 9.458727 CATATGGACAATTTCTATCTAAGCCAT 57.541 33.333 0.00 0.00 36.48 4.40
685 689 1.982395 CCAGCTCTACCGTCACCCA 60.982 63.158 0.00 0.00 0.00 4.51
1016 1699 2.973694 AATGGCATCAGATTTGTGGC 57.026 45.000 0.00 5.77 38.72 5.01
1215 1903 2.711009 TGTTCACCTCACCATTCTCCTT 59.289 45.455 0.00 0.00 0.00 3.36
1375 2076 6.014242 GGGTATGTCATCATCATCTCCACTAA 60.014 42.308 0.00 0.00 35.70 2.24
1618 2320 5.458041 AAAGCAATCAAAGTGCACTACAT 57.542 34.783 22.01 9.50 44.74 2.29
2028 2764 1.301795 GTTAGATAGGCGGCTGGGC 60.302 63.158 23.55 10.53 42.69 5.36
2029 2765 1.371558 GGTTAGATAGGCGGCTGGG 59.628 63.158 23.55 0.00 0.00 4.45
2030 2766 1.122019 AGGGTTAGATAGGCGGCTGG 61.122 60.000 23.55 0.00 0.00 4.85
2031 2767 1.546476 CTAGGGTTAGATAGGCGGCTG 59.454 57.143 23.55 0.00 0.00 4.85
2032 2768 1.550409 CCTAGGGTTAGATAGGCGGCT 60.550 57.143 18.33 18.33 32.60 5.52
2033 2769 0.896226 CCTAGGGTTAGATAGGCGGC 59.104 60.000 0.00 0.00 32.60 6.53
2034 2770 2.169330 GACCTAGGGTTAGATAGGCGG 58.831 57.143 14.81 0.00 42.04 6.13
2035 2771 2.169330 GGACCTAGGGTTAGATAGGCG 58.831 57.143 14.81 0.00 42.04 5.52
2036 2772 2.169330 CGGACCTAGGGTTAGATAGGC 58.831 57.143 14.81 0.00 42.04 3.93
2037 2773 3.419943 GTCGGACCTAGGGTTAGATAGG 58.580 54.545 14.81 0.00 43.61 2.57
2038 2774 3.419943 GGTCGGACCTAGGGTTAGATAG 58.580 54.545 19.92 0.00 35.25 2.08
2039 2775 2.108952 GGGTCGGACCTAGGGTTAGATA 59.891 54.545 25.39 0.00 38.64 1.98
2040 2776 1.133231 GGGTCGGACCTAGGGTTAGAT 60.133 57.143 25.39 0.00 38.64 1.98
2041 2777 0.259938 GGGTCGGACCTAGGGTTAGA 59.740 60.000 25.39 4.06 38.64 2.10
2042 2778 0.758310 GGGGTCGGACCTAGGGTTAG 60.758 65.000 25.39 1.48 38.64 2.34
2043 2779 1.311059 GGGGTCGGACCTAGGGTTA 59.689 63.158 25.39 0.00 38.64 2.85
2044 2780 2.040114 GGGGTCGGACCTAGGGTT 59.960 66.667 25.39 0.00 38.64 4.11
2045 2781 4.085546 GGGGGTCGGACCTAGGGT 62.086 72.222 25.39 0.00 38.64 4.34
2046 2782 3.752816 GAGGGGGTCGGACCTAGGG 62.753 73.684 25.39 0.00 38.64 3.53
2047 2783 2.123382 GAGGGGGTCGGACCTAGG 60.123 72.222 25.39 7.41 38.64 3.02
2048 2784 2.518825 CGAGGGGGTCGGACCTAG 60.519 72.222 25.39 9.68 45.58 3.02
2056 2792 1.380650 AGAGAAGAGCGAGGGGGTC 60.381 63.158 0.00 0.00 43.56 4.46
2057 2793 1.380650 GAGAGAAGAGCGAGGGGGT 60.381 63.158 0.00 0.00 0.00 4.95
2058 2794 2.485795 CGAGAGAAGAGCGAGGGGG 61.486 68.421 0.00 0.00 0.00 5.40
2059 2795 1.452289 TCGAGAGAAGAGCGAGGGG 60.452 63.158 0.00 0.00 37.03 4.79
2060 2796 4.227197 TCGAGAGAAGAGCGAGGG 57.773 61.111 0.00 0.00 37.03 4.30
2071 2807 1.544724 GAGGGAGATGGGATCGAGAG 58.455 60.000 0.00 0.00 0.00 3.20
2072 2808 0.113385 GGAGGGAGATGGGATCGAGA 59.887 60.000 0.00 0.00 0.00 4.04
2073 2809 0.178950 TGGAGGGAGATGGGATCGAG 60.179 60.000 0.00 0.00 0.00 4.04
2074 2810 0.178950 CTGGAGGGAGATGGGATCGA 60.179 60.000 0.00 0.00 0.00 3.59
2075 2811 1.825281 GCTGGAGGGAGATGGGATCG 61.825 65.000 0.00 0.00 0.00 3.69
2076 2812 1.825281 CGCTGGAGGGAGATGGGATC 61.825 65.000 0.00 0.00 0.00 3.36
2077 2813 1.840650 CGCTGGAGGGAGATGGGAT 60.841 63.158 0.00 0.00 0.00 3.85
2078 2814 2.444706 CGCTGGAGGGAGATGGGA 60.445 66.667 0.00 0.00 0.00 4.37
2079 2815 4.247380 GCGCTGGAGGGAGATGGG 62.247 72.222 0.00 0.00 0.00 4.00
2080 2816 4.247380 GGCGCTGGAGGGAGATGG 62.247 72.222 7.64 0.00 0.00 3.51
2081 2817 4.598894 CGGCGCTGGAGGGAGATG 62.599 72.222 8.83 0.00 0.00 2.90
2094 2830 3.792053 GATCAGGGTACTGGCGGCG 62.792 68.421 0.51 0.51 44.99 6.46
2095 2831 2.109181 GATCAGGGTACTGGCGGC 59.891 66.667 0.00 0.00 44.99 6.53
2096 2832 2.808206 GGGATCAGGGTACTGGCGG 61.808 68.421 0.00 0.00 44.99 6.13
2097 2833 2.808206 GGGGATCAGGGTACTGGCG 61.808 68.421 0.00 0.00 44.99 5.69
2098 2834 1.062488 ATGGGGATCAGGGTACTGGC 61.062 60.000 0.00 0.00 44.99 4.85
2099 2835 1.059913 GATGGGGATCAGGGTACTGG 58.940 60.000 0.00 0.00 44.99 4.00
2100 2836 1.974236 GAGATGGGGATCAGGGTACTG 59.026 57.143 0.00 0.00 46.30 2.74
2101 2837 1.132689 GGAGATGGGGATCAGGGTACT 60.133 57.143 0.00 0.00 0.00 2.73
2102 2838 1.353091 GGAGATGGGGATCAGGGTAC 58.647 60.000 0.00 0.00 0.00 3.34
2103 2839 0.193574 GGGAGATGGGGATCAGGGTA 59.806 60.000 0.00 0.00 0.00 3.69
2104 2840 1.073397 GGGAGATGGGGATCAGGGT 60.073 63.158 0.00 0.00 0.00 4.34
2105 2841 0.839853 GAGGGAGATGGGGATCAGGG 60.840 65.000 0.00 0.00 0.00 4.45
2106 2842 0.839853 GGAGGGAGATGGGGATCAGG 60.840 65.000 0.00 0.00 0.00 3.86
2107 2843 1.190833 CGGAGGGAGATGGGGATCAG 61.191 65.000 0.00 0.00 0.00 2.90
2108 2844 1.152247 CGGAGGGAGATGGGGATCA 60.152 63.158 0.00 0.00 0.00 2.92
2109 2845 2.588201 GCGGAGGGAGATGGGGATC 61.588 68.421 0.00 0.00 0.00 3.36
2110 2846 2.527875 GCGGAGGGAGATGGGGAT 60.528 66.667 0.00 0.00 0.00 3.85
2111 2847 3.758133 GAGCGGAGGGAGATGGGGA 62.758 68.421 0.00 0.00 0.00 4.81
2112 2848 3.237741 GAGCGGAGGGAGATGGGG 61.238 72.222 0.00 0.00 0.00 4.96
2113 2849 3.610669 CGAGCGGAGGGAGATGGG 61.611 72.222 0.00 0.00 0.00 4.00
2114 2850 1.872197 GATCGAGCGGAGGGAGATGG 61.872 65.000 0.00 0.00 0.00 3.51
2115 2851 0.893270 AGATCGAGCGGAGGGAGATG 60.893 60.000 0.00 0.00 0.00 2.90
2116 2852 0.608035 GAGATCGAGCGGAGGGAGAT 60.608 60.000 0.00 0.00 0.00 2.75
2117 2853 1.228003 GAGATCGAGCGGAGGGAGA 60.228 63.158 0.00 0.00 0.00 3.71
2118 2854 2.265182 GGAGATCGAGCGGAGGGAG 61.265 68.421 0.00 0.00 0.00 4.30
2119 2855 2.203365 GGAGATCGAGCGGAGGGA 60.203 66.667 0.00 0.00 0.00 4.20
2120 2856 2.203422 AGGAGATCGAGCGGAGGG 60.203 66.667 0.00 0.00 0.00 4.30
2121 2857 2.265182 GGAGGAGATCGAGCGGAGG 61.265 68.421 0.00 0.00 0.00 4.30
2122 2858 1.228124 AGGAGGAGATCGAGCGGAG 60.228 63.158 0.00 0.00 0.00 4.63
2123 2859 1.228003 GAGGAGGAGATCGAGCGGA 60.228 63.158 0.00 0.00 0.00 5.54
2124 2860 1.514678 CTGAGGAGGAGATCGAGCGG 61.515 65.000 0.00 0.00 0.00 5.52
2125 2861 1.948508 CTGAGGAGGAGATCGAGCG 59.051 63.158 0.00 0.00 0.00 5.03
2126 2862 1.659794 GCTGAGGAGGAGATCGAGC 59.340 63.158 0.00 0.00 0.00 5.03
2127 2863 0.178992 AGGCTGAGGAGGAGATCGAG 60.179 60.000 0.00 0.00 0.00 4.04
2128 2864 0.179004 GAGGCTGAGGAGGAGATCGA 60.179 60.000 0.00 0.00 0.00 3.59
2129 2865 0.178992 AGAGGCTGAGGAGGAGATCG 60.179 60.000 0.00 0.00 0.00 3.69
2130 2866 1.620822 GAGAGGCTGAGGAGGAGATC 58.379 60.000 0.00 0.00 0.00 2.75
2131 2867 0.178992 CGAGAGGCTGAGGAGGAGAT 60.179 60.000 0.00 0.00 0.00 2.75
2132 2868 1.225983 CGAGAGGCTGAGGAGGAGA 59.774 63.158 0.00 0.00 0.00 3.71
2133 2869 0.178992 ATCGAGAGGCTGAGGAGGAG 60.179 60.000 0.00 0.00 0.00 3.69
2134 2870 0.179004 GATCGAGAGGCTGAGGAGGA 60.179 60.000 0.00 0.00 0.00 3.71
2135 2871 0.178992 AGATCGAGAGGCTGAGGAGG 60.179 60.000 0.00 0.00 0.00 4.30
2136 2872 1.238439 GAGATCGAGAGGCTGAGGAG 58.762 60.000 0.00 0.00 0.00 3.69
2137 2873 0.179004 GGAGATCGAGAGGCTGAGGA 60.179 60.000 0.00 0.00 0.00 3.71
2138 2874 1.178534 GGGAGATCGAGAGGCTGAGG 61.179 65.000 0.00 0.00 0.00 3.86
2139 2875 0.467106 TGGGAGATCGAGAGGCTGAG 60.467 60.000 0.00 0.00 0.00 3.35
2140 2876 0.753479 GTGGGAGATCGAGAGGCTGA 60.753 60.000 0.00 0.00 0.00 4.26
2141 2877 1.039785 TGTGGGAGATCGAGAGGCTG 61.040 60.000 0.00 0.00 0.00 4.85
2142 2878 1.040339 GTGTGGGAGATCGAGAGGCT 61.040 60.000 0.00 0.00 0.00 4.58
2143 2879 1.439644 GTGTGGGAGATCGAGAGGC 59.560 63.158 0.00 0.00 0.00 4.70
2144 2880 1.730487 CGTGTGGGAGATCGAGAGG 59.270 63.158 0.00 0.00 0.00 3.69
2145 2881 1.064946 GCGTGTGGGAGATCGAGAG 59.935 63.158 0.00 0.00 0.00 3.20
2146 2882 1.037579 ATGCGTGTGGGAGATCGAGA 61.038 55.000 0.00 0.00 0.00 4.04
2147 2883 0.668535 TATGCGTGTGGGAGATCGAG 59.331 55.000 0.00 0.00 0.00 4.04
2148 2884 0.384309 GTATGCGTGTGGGAGATCGA 59.616 55.000 0.00 0.00 0.00 3.59
2149 2885 0.102300 TGTATGCGTGTGGGAGATCG 59.898 55.000 0.00 0.00 0.00 3.69
2150 2886 1.571919 GTGTATGCGTGTGGGAGATC 58.428 55.000 0.00 0.00 0.00 2.75
2151 2887 0.178068 GGTGTATGCGTGTGGGAGAT 59.822 55.000 0.00 0.00 0.00 2.75
2152 2888 1.594833 GGTGTATGCGTGTGGGAGA 59.405 57.895 0.00 0.00 0.00 3.71
2153 2889 1.449601 GGGTGTATGCGTGTGGGAG 60.450 63.158 0.00 0.00 0.00 4.30
2154 2890 2.178876 CTGGGTGTATGCGTGTGGGA 62.179 60.000 0.00 0.00 0.00 4.37
2155 2891 1.745115 CTGGGTGTATGCGTGTGGG 60.745 63.158 0.00 0.00 0.00 4.61
2156 2892 2.398554 GCTGGGTGTATGCGTGTGG 61.399 63.158 0.00 0.00 0.00 4.17
2157 2893 2.739704 CGCTGGGTGTATGCGTGTG 61.740 63.158 0.00 0.00 44.00 3.82
2158 2894 2.434185 CGCTGGGTGTATGCGTGT 60.434 61.111 0.00 0.00 44.00 4.49
2162 2898 2.897350 GAGGCGCTGGGTGTATGC 60.897 66.667 7.64 0.00 0.00 3.14
2163 2899 2.203070 GGAGGCGCTGGGTGTATG 60.203 66.667 7.64 0.00 0.00 2.39
2164 2900 2.257409 CTTGGAGGCGCTGGGTGTAT 62.257 60.000 7.64 0.00 0.00 2.29
2165 2901 2.925706 TTGGAGGCGCTGGGTGTA 60.926 61.111 7.64 0.00 0.00 2.90
2166 2902 4.335647 CTTGGAGGCGCTGGGTGT 62.336 66.667 7.64 0.00 0.00 4.16
2170 2906 4.479993 CTCCCTTGGAGGCGCTGG 62.480 72.222 7.64 0.21 45.43 4.85
2171 2907 3.672295 GTCTCCCTTGGAGGCGCTG 62.672 68.421 7.64 0.00 44.80 5.18
2172 2908 3.394836 GTCTCCCTTGGAGGCGCT 61.395 66.667 7.64 0.00 44.80 5.92
2185 2921 3.607661 GAGGGGATCGGGCGTCTC 61.608 72.222 0.00 0.00 0.00 3.36
2194 2930 2.413765 GTCAGCGTCGAGGGGATC 59.586 66.667 7.31 0.00 0.00 3.36
2195 2931 3.148279 GGTCAGCGTCGAGGGGAT 61.148 66.667 7.31 0.00 0.00 3.85
2196 2932 4.361971 AGGTCAGCGTCGAGGGGA 62.362 66.667 7.31 0.00 0.00 4.81
2197 2933 3.827898 GAGGTCAGCGTCGAGGGG 61.828 72.222 7.31 0.00 0.00 4.79
2203 2939 2.125512 AATGCCGAGGTCAGCGTC 60.126 61.111 0.00 0.00 0.00 5.19
2204 2940 2.125512 GAATGCCGAGGTCAGCGT 60.126 61.111 0.00 0.00 0.00 5.07
2205 2941 3.257561 CGAATGCCGAGGTCAGCG 61.258 66.667 0.00 0.00 41.76 5.18
2206 2942 2.892425 CCGAATGCCGAGGTCAGC 60.892 66.667 0.00 0.00 41.76 4.26
2207 2943 2.892425 GCCGAATGCCGAGGTCAG 60.892 66.667 0.00 0.00 41.76 3.51
2216 2952 3.599704 GGCTCCATGGCCGAATGC 61.600 66.667 6.96 4.15 42.82 3.56
2237 2973 4.742201 CCTGCTGGTGGTCGTCGG 62.742 72.222 0.51 0.00 0.00 4.79
2238 2974 4.742201 CCCTGCTGGTGGTCGTCG 62.742 72.222 9.00 0.00 0.00 5.12
2276 3012 4.821589 GAAGGAGAGGCCGGCGTG 62.822 72.222 28.98 0.00 43.43 5.34
2279 3015 3.855853 GAGGAAGGAGAGGCCGGC 61.856 72.222 21.18 21.18 43.43 6.13
2280 3016 3.157949 GGAGGAAGGAGAGGCCGG 61.158 72.222 0.00 0.00 43.43 6.13
2281 3017 3.532155 CGGAGGAAGGAGAGGCCG 61.532 72.222 0.00 0.00 43.43 6.13
2282 3018 3.855853 GCGGAGGAAGGAGAGGCC 61.856 72.222 0.00 0.00 0.00 5.19
2283 3019 3.855853 GGCGGAGGAAGGAGAGGC 61.856 72.222 0.00 0.00 0.00 4.70
2284 3020 3.157949 GGGCGGAGGAAGGAGAGG 61.158 72.222 0.00 0.00 0.00 3.69
2285 3021 1.990060 TTGGGCGGAGGAAGGAGAG 60.990 63.158 0.00 0.00 0.00 3.20
2286 3022 2.121832 TTGGGCGGAGGAAGGAGA 59.878 61.111 0.00 0.00 0.00 3.71
2287 3023 2.269241 GTTGGGCGGAGGAAGGAG 59.731 66.667 0.00 0.00 0.00 3.69
2288 3024 3.327404 GGTTGGGCGGAGGAAGGA 61.327 66.667 0.00 0.00 0.00 3.36
2289 3025 3.330720 AGGTTGGGCGGAGGAAGG 61.331 66.667 0.00 0.00 0.00 3.46
2290 3026 2.269241 GAGGTTGGGCGGAGGAAG 59.731 66.667 0.00 0.00 0.00 3.46
2291 3027 2.528127 TGAGGTTGGGCGGAGGAA 60.528 61.111 0.00 0.00 0.00 3.36
2292 3028 3.003173 CTGAGGTTGGGCGGAGGA 61.003 66.667 0.00 0.00 0.00 3.71
2293 3029 4.785453 GCTGAGGTTGGGCGGAGG 62.785 72.222 0.00 0.00 0.00 4.30
2294 3030 4.785453 GGCTGAGGTTGGGCGGAG 62.785 72.222 0.00 0.00 0.00 4.63
2296 3032 4.431131 ATGGCTGAGGTTGGGCGG 62.431 66.667 0.00 0.00 0.00 6.13
2297 3033 3.136123 CATGGCTGAGGTTGGGCG 61.136 66.667 0.00 0.00 0.00 6.13
2298 3034 2.757099 CCATGGCTGAGGTTGGGC 60.757 66.667 0.00 0.00 0.00 5.36
2299 3035 1.379044 GTCCATGGCTGAGGTTGGG 60.379 63.158 6.96 0.00 0.00 4.12
2300 3036 1.746615 CGTCCATGGCTGAGGTTGG 60.747 63.158 6.96 0.00 0.00 3.77
2301 3037 1.003355 ACGTCCATGGCTGAGGTTG 60.003 57.895 6.96 0.00 0.00 3.77
2302 3038 1.003355 CACGTCCATGGCTGAGGTT 60.003 57.895 6.96 0.00 0.00 3.50
2303 3039 2.665000 CACGTCCATGGCTGAGGT 59.335 61.111 6.96 0.00 0.00 3.85
2304 3040 2.821366 GCACGTCCATGGCTGAGG 60.821 66.667 6.96 0.00 0.00 3.86
2305 3041 2.046988 TGCACGTCCATGGCTGAG 60.047 61.111 6.96 1.31 0.00 3.35
2306 3042 2.358615 GTGCACGTCCATGGCTGA 60.359 61.111 6.96 0.00 0.00 4.26
2307 3043 2.359107 AGTGCACGTCCATGGCTG 60.359 61.111 12.01 3.96 0.00 4.85
2308 3044 2.359107 CAGTGCACGTCCATGGCT 60.359 61.111 12.01 0.00 0.00 4.75
2309 3045 4.107051 GCAGTGCACGTCCATGGC 62.107 66.667 11.09 0.96 0.00 4.40
2310 3046 3.434319 GGCAGTGCACGTCCATGG 61.434 66.667 18.61 4.97 0.00 3.66
2311 3047 3.792047 CGGCAGTGCACGTCCATG 61.792 66.667 23.69 13.35 0.00 3.66
2314 3050 4.735132 TAGCGGCAGTGCACGTCC 62.735 66.667 18.61 15.13 37.31 4.79
2315 3051 3.479269 GTAGCGGCAGTGCACGTC 61.479 66.667 18.61 13.23 37.31 4.34
2316 3052 3.916392 GAGTAGCGGCAGTGCACGT 62.916 63.158 18.61 10.81 37.31 4.49
2317 3053 3.181967 GAGTAGCGGCAGTGCACG 61.182 66.667 18.61 18.30 37.31 5.34
2318 3054 2.097038 CAGAGTAGCGGCAGTGCAC 61.097 63.158 18.61 9.40 37.31 4.57
2319 3055 2.262603 CAGAGTAGCGGCAGTGCA 59.737 61.111 18.61 0.00 37.31 4.57
2320 3056 3.191539 GCAGAGTAGCGGCAGTGC 61.192 66.667 6.55 6.55 37.65 4.40
2321 3057 1.808799 CAGCAGAGTAGCGGCAGTG 60.809 63.158 1.45 0.00 40.40 3.66
2322 3058 2.575993 CAGCAGAGTAGCGGCAGT 59.424 61.111 1.45 0.00 40.40 4.40
2359 3095 3.423154 CAAAGGAGCGGGCGTGAC 61.423 66.667 0.00 0.00 0.00 3.67
2364 3100 3.976701 TAGCAGCAAAGGAGCGGGC 62.977 63.158 0.00 0.00 40.15 6.13
2365 3101 2.109126 GTAGCAGCAAAGGAGCGGG 61.109 63.158 0.00 0.00 40.15 6.13
2366 3102 2.109126 GGTAGCAGCAAAGGAGCGG 61.109 63.158 0.00 0.00 40.15 5.52
2367 3103 2.109126 GGGTAGCAGCAAAGGAGCG 61.109 63.158 0.00 0.00 40.15 5.03
2368 3104 2.109126 CGGGTAGCAGCAAAGGAGC 61.109 63.158 0.00 0.00 0.00 4.70
2369 3105 1.450312 CCGGGTAGCAGCAAAGGAG 60.450 63.158 0.00 0.00 0.00 3.69
2370 3106 1.916273 TCCGGGTAGCAGCAAAGGA 60.916 57.895 0.00 0.00 0.00 3.36
2371 3107 1.745489 GTCCGGGTAGCAGCAAAGG 60.745 63.158 0.00 0.00 0.00 3.11
2372 3108 2.100631 CGTCCGGGTAGCAGCAAAG 61.101 63.158 0.00 0.00 0.00 2.77
2373 3109 2.047655 CGTCCGGGTAGCAGCAAA 60.048 61.111 0.00 0.00 0.00 3.68
2374 3110 3.291101 GACGTCCGGGTAGCAGCAA 62.291 63.158 3.51 0.00 0.00 3.91
2375 3111 3.755628 GACGTCCGGGTAGCAGCA 61.756 66.667 3.51 0.00 0.00 4.41
2376 3112 4.509737 GGACGTCCGGGTAGCAGC 62.510 72.222 20.85 0.00 0.00 5.25
2377 3113 3.834799 GGGACGTCCGGGTAGCAG 61.835 72.222 27.68 0.00 36.71 4.24
2378 3114 4.371417 AGGGACGTCCGGGTAGCA 62.371 66.667 27.68 0.00 41.52 3.49
2379 3115 3.834799 CAGGGACGTCCGGGTAGC 61.835 72.222 27.68 13.07 41.52 3.58
2380 3116 3.834799 GCAGGGACGTCCGGGTAG 61.835 72.222 27.68 15.69 41.52 3.18
2399 3135 3.730761 CACTCTGGCGCACTTGGC 61.731 66.667 10.83 0.00 39.90 4.52
2400 3136 3.730761 GCACTCTGGCGCACTTGG 61.731 66.667 10.83 0.00 0.00 3.61
2401 3137 3.730761 GGCACTCTGGCGCACTTG 61.731 66.667 10.83 0.00 31.79 3.16
2457 3193 3.069318 AACTCGGAGCTCGGGGAC 61.069 66.667 26.40 2.39 45.25 4.46
2458 3194 3.068691 CAACTCGGAGCTCGGGGA 61.069 66.667 26.40 13.43 45.25 4.81
2459 3195 4.148825 CCAACTCGGAGCTCGGGG 62.149 72.222 18.92 18.92 45.25 5.73
2460 3196 4.821589 GCCAACTCGGAGCTCGGG 62.822 72.222 19.94 12.00 46.65 5.14
2461 3197 4.821589 GGCCAACTCGGAGCTCGG 62.822 72.222 14.80 14.80 39.77 4.63
2501 3237 2.343163 CTGATCACCGGCGAGAGGAC 62.343 65.000 9.30 3.11 0.00 3.85
2502 3238 2.044352 TGATCACCGGCGAGAGGA 60.044 61.111 9.30 0.00 0.00 3.71
2503 3239 2.415010 CTGATCACCGGCGAGAGG 59.585 66.667 9.30 0.00 0.00 3.69
2504 3240 2.279120 GCTGATCACCGGCGAGAG 60.279 66.667 9.30 0.00 37.42 3.20
2509 3245 3.044059 GCTTGTGCTGATCACCGGC 62.044 63.158 0.00 0.00 45.03 6.13
2510 3246 1.642037 CTGCTTGTGCTGATCACCGG 61.642 60.000 0.00 0.00 45.03 5.28
2511 3247 1.642037 CCTGCTTGTGCTGATCACCG 61.642 60.000 0.00 0.00 45.03 4.94
2512 3248 0.607489 ACCTGCTTGTGCTGATCACC 60.607 55.000 0.00 0.00 45.03 4.02
2513 3249 0.801251 GACCTGCTTGTGCTGATCAC 59.199 55.000 0.00 0.00 45.82 3.06
2514 3250 0.397564 TGACCTGCTTGTGCTGATCA 59.602 50.000 0.00 0.00 38.17 2.92
2515 3251 1.669779 GATGACCTGCTTGTGCTGATC 59.330 52.381 0.00 0.00 40.01 2.92
2516 3252 1.681166 GGATGACCTGCTTGTGCTGAT 60.681 52.381 0.00 0.00 40.01 2.90
2517 3253 0.321919 GGATGACCTGCTTGTGCTGA 60.322 55.000 0.00 0.00 40.01 4.26
2518 3254 0.322277 AGGATGACCTGCTTGTGCTG 60.322 55.000 0.00 0.00 45.92 4.41
2519 3255 2.073232 AGGATGACCTGCTTGTGCT 58.927 52.632 0.00 0.00 45.92 4.40
2520 3256 4.730487 AGGATGACCTGCTTGTGC 57.270 55.556 0.00 0.00 45.92 4.57
2542 3278 4.436998 CCTCCTGGTGACGGCGAC 62.437 72.222 16.62 8.59 34.42 5.19
2543 3279 4.671590 TCCTCCTGGTGACGGCGA 62.672 66.667 16.62 0.00 34.42 5.54
2544 3280 4.135153 CTCCTCCTGGTGACGGCG 62.135 72.222 4.80 4.80 34.42 6.46
2545 3281 4.459089 GCTCCTCCTGGTGACGGC 62.459 72.222 0.00 0.00 34.42 5.68
2546 3282 2.681778 AGCTCCTCCTGGTGACGG 60.682 66.667 0.00 0.00 34.23 4.79
2547 3283 2.888863 GAGCTCCTCCTGGTGACG 59.111 66.667 0.87 0.00 34.23 4.35
2548 3284 1.939769 GACGAGCTCCTCCTGGTGAC 61.940 65.000 8.47 0.00 34.23 3.67
2549 3285 1.679305 GACGAGCTCCTCCTGGTGA 60.679 63.158 8.47 0.00 34.23 4.02
2550 3286 2.716017 GGACGAGCTCCTCCTGGTG 61.716 68.421 20.81 2.35 35.89 4.17
2551 3287 2.363147 GGACGAGCTCCTCCTGGT 60.363 66.667 20.81 6.92 35.89 4.00


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

AutoCloner maintained by Alex Coulton.