Multiple sequence alignment - TraesCS3A01G415900

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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 TraesCS3A01G415900 chr3A 100.000 2167 0 0 791 2957 658843754 658841588 0.000000e+00 4002.0
1 TraesCS3A01G415900 chr3A 100.000 439 0 0 1 439 658844544 658844106 0.000000e+00 811.0
2 TraesCS3A01G415900 chr3D 90.273 2015 88 38 987 2957 524201750 524203700 0.000000e+00 2536.0
3 TraesCS3A01G415900 chr3D 82.736 307 18 10 130 414 524201247 524201540 1.060000e-59 241.0
4 TraesCS3A01G415900 chr3B 90.040 1998 95 39 985 2957 691459171 691457253 0.000000e+00 2492.0
5 TraesCS3A01G415900 chr3B 86.056 251 17 8 129 375 691459636 691459400 1.360000e-63 254.0
6 TraesCS3A01G415900 chr3B 91.736 121 7 2 791 911 691459328 691459211 6.560000e-37 165.0
7 TraesCS3A01G415900 chr3B 94.595 37 2 0 384 420 691459408 691459372 1.140000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G415900 chr3A 658841588 658844544 2956 True 2406.50 4002 100.00000 1 2957 2 chr3A.!!$R1 2956
1 TraesCS3A01G415900 chr3D 524201247 524203700 2453 False 1388.50 2536 86.50450 130 2957 2 chr3D.!!$F1 2827
2 TraesCS3A01G415900 chr3B 691457253 691459636 2383 True 742.35 2492 90.60675 129 2957 4 chr3B.!!$R1 2828

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
974 1004 0.034059 CTAGTGGATAGGCGCCTTGG 59.966 60.0 37.74 14.04 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2697 2786 0.035056 CCAGTGGACATCCCTGAACC 60.035 60.0 1.68 0.0 36.83 3.62 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
31 32 2.363795 CGAGCCCCCAGGACAGTA 60.364 66.667 0.00 0.00 33.47 2.74
32 33 1.987855 CGAGCCCCCAGGACAGTAA 60.988 63.158 0.00 0.00 33.47 2.24
33 34 1.602771 GAGCCCCCAGGACAGTAAC 59.397 63.158 0.00 0.00 33.47 2.50
34 35 1.911702 GAGCCCCCAGGACAGTAACC 61.912 65.000 0.00 0.00 33.47 2.85
35 36 2.980177 GCCCCCAGGACAGTAACCC 61.980 68.421 0.00 0.00 33.47 4.11
36 37 2.306384 CCCCCAGGACAGTAACCCC 61.306 68.421 0.00 0.00 33.47 4.95
37 38 2.666098 CCCCAGGACAGTAACCCCG 61.666 68.421 0.00 0.00 0.00 5.73
38 39 1.611261 CCCAGGACAGTAACCCCGA 60.611 63.158 0.00 0.00 0.00 5.14
39 40 1.614241 CCCAGGACAGTAACCCCGAG 61.614 65.000 0.00 0.00 0.00 4.63
40 41 1.218316 CAGGACAGTAACCCCGAGC 59.782 63.158 0.00 0.00 0.00 5.03
41 42 1.078710 AGGACAGTAACCCCGAGCT 59.921 57.895 0.00 0.00 0.00 4.09
42 43 0.971447 AGGACAGTAACCCCGAGCTC 60.971 60.000 2.73 2.73 0.00 4.09
43 44 1.255667 GGACAGTAACCCCGAGCTCA 61.256 60.000 15.40 0.00 0.00 4.26
44 45 0.108756 GACAGTAACCCCGAGCTCAC 60.109 60.000 15.40 2.80 0.00 3.51
45 46 1.218316 CAGTAACCCCGAGCTCACC 59.782 63.158 15.40 0.00 0.00 4.02
46 47 2.183555 GTAACCCCGAGCTCACCG 59.816 66.667 15.40 0.00 0.00 4.94
47 48 3.766691 TAACCCCGAGCTCACCGC 61.767 66.667 15.40 0.00 39.57 5.68
53 54 3.764466 CGAGCTCACCGCCCTCTT 61.764 66.667 15.40 0.00 40.39 2.85
54 55 2.415608 CGAGCTCACCGCCCTCTTA 61.416 63.158 15.40 0.00 40.39 2.10
55 56 1.142097 GAGCTCACCGCCCTCTTAC 59.858 63.158 9.40 0.00 40.39 2.34
56 57 2.187163 GCTCACCGCCCTCTTACC 59.813 66.667 0.00 0.00 0.00 2.85
57 58 2.359967 GCTCACCGCCCTCTTACCT 61.360 63.158 0.00 0.00 0.00 3.08
58 59 1.517832 CTCACCGCCCTCTTACCTG 59.482 63.158 0.00 0.00 0.00 4.00
59 60 0.970937 CTCACCGCCCTCTTACCTGA 60.971 60.000 0.00 0.00 0.00 3.86
60 61 0.970937 TCACCGCCCTCTTACCTGAG 60.971 60.000 0.00 0.00 0.00 3.35
61 62 0.970937 CACCGCCCTCTTACCTGAGA 60.971 60.000 0.00 0.00 36.23 3.27
62 63 0.971447 ACCGCCCTCTTACCTGAGAC 60.971 60.000 0.00 0.00 36.23 3.36
63 64 1.677637 CCGCCCTCTTACCTGAGACC 61.678 65.000 0.00 0.00 36.23 3.85
64 65 1.817209 GCCCTCTTACCTGAGACCG 59.183 63.158 0.00 0.00 36.23 4.79
65 66 0.683504 GCCCTCTTACCTGAGACCGA 60.684 60.000 0.00 0.00 36.23 4.69
66 67 1.394618 CCCTCTTACCTGAGACCGAG 58.605 60.000 0.00 0.00 36.23 4.63
67 68 1.064611 CCCTCTTACCTGAGACCGAGA 60.065 57.143 0.00 0.00 36.23 4.04
68 69 2.294074 CCTCTTACCTGAGACCGAGAG 58.706 57.143 0.00 0.00 36.23 3.20
69 70 1.673920 CTCTTACCTGAGACCGAGAGC 59.326 57.143 0.00 0.00 36.23 4.09
70 71 0.741915 CTTACCTGAGACCGAGAGCC 59.258 60.000 0.00 0.00 0.00 4.70
71 72 0.039180 TTACCTGAGACCGAGAGCCA 59.961 55.000 0.00 0.00 0.00 4.75
72 73 0.259065 TACCTGAGACCGAGAGCCAT 59.741 55.000 0.00 0.00 0.00 4.40
73 74 1.040339 ACCTGAGACCGAGAGCCATC 61.040 60.000 0.00 0.00 0.00 3.51
74 75 1.358402 CTGAGACCGAGAGCCATCG 59.642 63.158 1.32 1.32 42.36 3.84
102 103 4.148825 GCCATGGCCTCTCGTCGT 62.149 66.667 27.24 0.00 34.56 4.34
103 104 2.105128 CCATGGCCTCTCGTCGTC 59.895 66.667 3.32 0.00 0.00 4.20
104 105 2.278206 CATGGCCTCTCGTCGTCG 60.278 66.667 3.32 0.00 38.55 5.12
105 106 2.437895 ATGGCCTCTCGTCGTCGA 60.438 61.111 3.32 4.42 44.12 4.20
106 107 1.824329 ATGGCCTCTCGTCGTCGAT 60.824 57.895 3.32 0.00 45.21 3.59
107 108 0.534427 ATGGCCTCTCGTCGTCGATA 60.534 55.000 3.32 0.00 45.21 2.92
108 109 1.279238 GGCCTCTCGTCGTCGATAC 59.721 63.158 5.00 0.00 45.21 2.24
109 110 1.159098 GGCCTCTCGTCGTCGATACT 61.159 60.000 5.00 0.00 45.21 2.12
110 111 0.232816 GCCTCTCGTCGTCGATACTC 59.767 60.000 5.00 0.00 45.21 2.59
111 112 1.568606 CCTCTCGTCGTCGATACTCA 58.431 55.000 5.00 0.00 45.21 3.41
112 113 2.136728 CCTCTCGTCGTCGATACTCAT 58.863 52.381 5.00 0.00 45.21 2.90
113 114 2.096664 CCTCTCGTCGTCGATACTCATG 60.097 54.545 5.00 0.00 45.21 3.07
114 115 1.865340 TCTCGTCGTCGATACTCATGG 59.135 52.381 5.00 0.00 45.21 3.66
115 116 1.598132 CTCGTCGTCGATACTCATGGT 59.402 52.381 5.00 0.00 45.21 3.55
116 117 1.329599 TCGTCGTCGATACTCATGGTG 59.670 52.381 0.00 0.00 41.35 4.17
117 118 1.329599 CGTCGTCGATACTCATGGTGA 59.670 52.381 0.00 0.00 39.71 4.02
118 119 2.223180 CGTCGTCGATACTCATGGTGAA 60.223 50.000 0.00 0.00 39.71 3.18
119 120 3.729762 CGTCGTCGATACTCATGGTGAAA 60.730 47.826 0.00 0.00 39.71 2.69
120 121 3.546670 GTCGTCGATACTCATGGTGAAAC 59.453 47.826 0.00 0.00 0.00 2.78
121 122 3.442625 TCGTCGATACTCATGGTGAAACT 59.557 43.478 0.00 0.00 36.74 2.66
122 123 4.082408 TCGTCGATACTCATGGTGAAACTT 60.082 41.667 0.00 0.00 36.74 2.66
123 124 4.031765 CGTCGATACTCATGGTGAAACTTG 59.968 45.833 0.00 0.00 36.74 3.16
124 125 4.330074 GTCGATACTCATGGTGAAACTTGG 59.670 45.833 0.00 0.00 36.74 3.61
125 126 3.623060 CGATACTCATGGTGAAACTTGGG 59.377 47.826 0.00 0.00 36.74 4.12
126 127 4.622933 CGATACTCATGGTGAAACTTGGGA 60.623 45.833 0.00 0.00 36.74 4.37
127 128 3.146104 ACTCATGGTGAAACTTGGGAG 57.854 47.619 0.00 0.00 36.74 4.30
141 142 4.313282 ACTTGGGAGCGTAGTAGAAAAAC 58.687 43.478 0.00 0.00 0.00 2.43
153 154 9.577003 GCGTAGTAGAAAAACGGAAAATATATG 57.423 33.333 0.00 0.00 37.12 1.78
158 161 9.103048 GTAGAAAAACGGAAAATATATGCGATG 57.897 33.333 8.90 0.00 35.47 3.84
186 189 2.490115 GGATCGGAGGAGCATAGTGTAG 59.510 54.545 0.00 0.00 0.00 2.74
269 272 2.021380 CGCACGCATTTACTCGCC 59.979 61.111 0.00 0.00 0.00 5.54
272 275 2.510691 ACGCATTTACTCGCCCCG 60.511 61.111 0.00 0.00 0.00 5.73
326 351 1.081972 CCCGGTTTAAAACGCCACG 60.082 57.895 20.13 6.40 0.00 4.94
416 441 2.950194 GTTCGGCTCGCTCGCTAC 60.950 66.667 0.00 0.00 0.00 3.58
420 445 3.917760 GGCTCGCTCGCTACCCAT 61.918 66.667 0.00 0.00 0.00 4.00
421 446 2.561956 GGCTCGCTCGCTACCCATA 61.562 63.158 0.00 0.00 0.00 2.74
422 447 1.081108 GCTCGCTCGCTACCCATAG 60.081 63.158 0.00 0.00 0.00 2.23
432 457 2.721971 CTACCCATAGCCAGCCAGCG 62.722 65.000 0.00 0.00 38.01 5.18
434 459 2.590007 CCATAGCCAGCCAGCGTC 60.590 66.667 0.00 0.00 38.01 5.19
435 460 2.503061 CATAGCCAGCCAGCGTCT 59.497 61.111 0.00 0.00 38.01 4.18
438 463 3.965026 TAGCCAGCCAGCGTCTCCT 62.965 63.158 0.00 0.00 38.01 3.69
876 901 1.804326 CGCCGCCGCCTATGTATAC 60.804 63.158 0.00 0.00 0.00 1.47
887 912 4.096682 CGCCTATGTATACTAGCCTTCCTC 59.903 50.000 4.17 0.00 0.00 3.71
888 913 4.403113 GCCTATGTATACTAGCCTTCCTCC 59.597 50.000 4.17 0.00 0.00 4.30
889 914 5.811697 GCCTATGTATACTAGCCTTCCTCCT 60.812 48.000 4.17 0.00 0.00 3.69
890 915 5.889289 CCTATGTATACTAGCCTTCCTCCTC 59.111 48.000 4.17 0.00 0.00 3.71
891 916 4.115398 TGTATACTAGCCTTCCTCCTCC 57.885 50.000 4.17 0.00 0.00 4.30
892 917 3.727923 TGTATACTAGCCTTCCTCCTCCT 59.272 47.826 4.17 0.00 0.00 3.69
893 918 4.170251 TGTATACTAGCCTTCCTCCTCCTT 59.830 45.833 4.17 0.00 0.00 3.36
894 919 5.374753 TGTATACTAGCCTTCCTCCTCCTTA 59.625 44.000 4.17 0.00 0.00 2.69
895 920 3.322191 ACTAGCCTTCCTCCTCCTTAG 57.678 52.381 0.00 0.00 0.00 2.18
896 921 1.967779 CTAGCCTTCCTCCTCCTTAGC 59.032 57.143 0.00 0.00 0.00 3.09
897 922 0.692756 AGCCTTCCTCCTCCTTAGCC 60.693 60.000 0.00 0.00 0.00 3.93
914 944 1.076677 AGCCCATCATTCATCCATCCC 59.923 52.381 0.00 0.00 0.00 3.85
916 946 1.615116 CCCATCATTCATCCATCCCCG 60.615 57.143 0.00 0.00 0.00 5.73
917 947 1.352017 CCATCATTCATCCATCCCCGA 59.648 52.381 0.00 0.00 0.00 5.14
929 959 1.040339 ATCCCCGAGTGTCTCTCAGC 61.040 60.000 3.01 0.00 42.88 4.26
936 966 1.135731 GTGTCTCTCAGCTCGTCGG 59.864 63.158 0.00 0.00 0.00 4.79
937 967 2.101380 GTCTCTCAGCTCGTCGGC 59.899 66.667 0.00 0.00 0.00 5.54
938 968 2.045829 TCTCTCAGCTCGTCGGCT 60.046 61.111 2.81 2.81 44.10 5.52
940 970 3.447634 CTCTCAGCTCGTCGGCTCG 62.448 68.421 5.39 3.20 41.00 5.03
941 971 3.805307 CTCAGCTCGTCGGCTCGT 61.805 66.667 5.39 0.00 41.00 4.18
942 972 3.726631 CTCAGCTCGTCGGCTCGTC 62.727 68.421 5.39 0.00 41.00 4.20
943 973 4.103103 CAGCTCGTCGGCTCGTCA 62.103 66.667 5.39 0.00 41.00 4.35
944 974 3.134792 AGCTCGTCGGCTCGTCAT 61.135 61.111 2.81 0.00 38.24 3.06
945 975 1.818363 AGCTCGTCGGCTCGTCATA 60.818 57.895 2.81 0.00 38.24 2.15
946 976 1.369448 GCTCGTCGGCTCGTCATAG 60.369 63.158 0.00 0.00 0.00 2.23
947 977 1.280142 CTCGTCGGCTCGTCATAGG 59.720 63.158 0.00 0.00 0.00 2.57
948 978 2.353607 CGTCGGCTCGTCATAGGC 60.354 66.667 0.00 0.00 38.63 3.93
949 979 2.835705 CGTCGGCTCGTCATAGGCT 61.836 63.158 0.00 0.00 39.79 4.58
950 980 1.008309 GTCGGCTCGTCATAGGCTC 60.008 63.158 0.00 0.00 39.79 4.70
951 981 1.453197 TCGGCTCGTCATAGGCTCA 60.453 57.895 0.00 0.00 39.79 4.26
952 982 0.823769 TCGGCTCGTCATAGGCTCAT 60.824 55.000 0.00 0.00 39.79 2.90
953 983 0.387878 CGGCTCGTCATAGGCTCATC 60.388 60.000 0.00 0.00 39.79 2.92
954 984 0.676184 GGCTCGTCATAGGCTCATCA 59.324 55.000 0.00 0.00 38.92 3.07
955 985 1.604185 GGCTCGTCATAGGCTCATCAC 60.604 57.143 0.00 0.00 38.92 3.06
956 986 1.339610 GCTCGTCATAGGCTCATCACT 59.660 52.381 0.00 0.00 0.00 3.41
957 987 2.554462 GCTCGTCATAGGCTCATCACTA 59.446 50.000 0.00 0.00 0.00 2.74
958 988 3.365868 GCTCGTCATAGGCTCATCACTAG 60.366 52.174 0.00 0.00 0.00 2.57
959 989 3.818210 CTCGTCATAGGCTCATCACTAGT 59.182 47.826 0.00 0.00 0.00 2.57
960 990 3.565902 TCGTCATAGGCTCATCACTAGTG 59.434 47.826 17.17 17.17 0.00 2.74
961 991 3.304996 CGTCATAGGCTCATCACTAGTGG 60.305 52.174 22.48 7.88 0.00 4.00
962 992 3.891977 GTCATAGGCTCATCACTAGTGGA 59.108 47.826 22.48 11.79 0.00 4.02
963 993 4.526262 GTCATAGGCTCATCACTAGTGGAT 59.474 45.833 22.48 11.73 0.00 3.41
964 994 5.712446 GTCATAGGCTCATCACTAGTGGATA 59.288 44.000 22.48 4.02 0.00 2.59
965 995 5.948758 TCATAGGCTCATCACTAGTGGATAG 59.051 44.000 22.48 16.51 37.53 2.08
966 996 3.505386 AGGCTCATCACTAGTGGATAGG 58.495 50.000 22.48 5.73 35.63 2.57
967 997 2.028567 GGCTCATCACTAGTGGATAGGC 60.029 54.545 22.48 21.65 35.63 3.93
968 998 2.352225 GCTCATCACTAGTGGATAGGCG 60.352 54.545 22.48 1.89 35.63 5.52
969 999 1.613925 TCATCACTAGTGGATAGGCGC 59.386 52.381 22.48 0.00 35.63 6.53
970 1000 0.969894 ATCACTAGTGGATAGGCGCC 59.030 55.000 21.89 21.89 35.63 6.53
971 1001 0.106167 TCACTAGTGGATAGGCGCCT 60.106 55.000 34.85 34.85 35.63 5.52
972 1002 0.753262 CACTAGTGGATAGGCGCCTT 59.247 55.000 37.74 22.46 35.63 4.35
973 1003 0.753262 ACTAGTGGATAGGCGCCTTG 59.247 55.000 37.74 12.11 35.63 3.61
974 1004 0.034059 CTAGTGGATAGGCGCCTTGG 59.966 60.000 37.74 14.04 0.00 3.61
975 1005 0.689745 TAGTGGATAGGCGCCTTGGT 60.690 55.000 37.74 21.44 0.00 3.67
976 1006 1.523938 GTGGATAGGCGCCTTGGTC 60.524 63.158 37.74 27.63 0.00 4.02
977 1007 2.280186 GGATAGGCGCCTTGGTCG 60.280 66.667 37.74 0.00 0.00 4.79
978 1008 2.792947 GGATAGGCGCCTTGGTCGA 61.793 63.158 37.74 16.84 0.00 4.20
979 1009 1.300233 GATAGGCGCCTTGGTCGAG 60.300 63.158 37.74 0.00 0.00 4.04
980 1010 2.017559 GATAGGCGCCTTGGTCGAGT 62.018 60.000 37.74 9.67 0.00 4.18
981 1011 2.017559 ATAGGCGCCTTGGTCGAGTC 62.018 60.000 37.74 0.00 0.00 3.36
1038 1068 2.492090 CCCTCCTGCTTCTCGTCG 59.508 66.667 0.00 0.00 0.00 5.12
1455 1500 1.138247 GGACTACTACGTGGCGGTG 59.862 63.158 0.00 0.00 0.00 4.94
1873 1918 1.101331 CTTCATCTTCAAGCCCCAGC 58.899 55.000 0.00 0.00 40.32 4.85
1960 2020 3.657634 GCATGGAAGATCGAATGAGCTA 58.342 45.455 0.00 0.00 40.73 3.32
1961 2021 3.679025 GCATGGAAGATCGAATGAGCTAG 59.321 47.826 0.00 0.00 40.73 3.42
1962 2022 4.560311 GCATGGAAGATCGAATGAGCTAGA 60.560 45.833 0.00 0.00 40.73 2.43
1963 2023 4.576216 TGGAAGATCGAATGAGCTAGAC 57.424 45.455 0.00 0.00 40.73 2.59
1964 2024 4.211125 TGGAAGATCGAATGAGCTAGACT 58.789 43.478 0.00 0.00 40.73 3.24
1980 2050 5.934935 CTAGACTTAGCTAGCTAGACACC 57.065 47.826 25.15 12.45 34.89 4.16
1983 2053 3.292460 ACTTAGCTAGCTAGACACCCTG 58.708 50.000 25.15 9.00 0.00 4.45
2023 2094 2.813179 CGCCACATTACAGAGCGGC 61.813 63.158 0.00 0.00 42.93 6.53
2049 2120 5.895636 TGATGGACATTTCACCATGTTAC 57.104 39.130 0.00 0.00 45.41 2.50
2062 2133 4.391830 CACCATGTTACGAGCAACATACTT 59.608 41.667 12.18 1.52 45.18 2.24
2088 2159 9.955208 TCTACCATGTAATGTAAGTATGTAACG 57.045 33.333 0.00 0.00 44.81 3.18
2089 2160 9.955208 CTACCATGTAATGTAAGTATGTAACGA 57.045 33.333 0.00 0.00 44.81 3.85
2091 2162 9.256477 ACCATGTAATGTAAGTATGTAACGATG 57.744 33.333 0.00 0.00 44.81 3.84
2092 2163 9.256477 CCATGTAATGTAAGTATGTAACGATGT 57.744 33.333 0.00 0.00 44.81 3.06
2094 2165 9.811995 ATGTAATGTAAGTATGTAACGATGTGT 57.188 29.630 0.00 0.00 0.00 3.72
2119 2190 2.571653 TGTAAGAGGGGGAGTGAATGTG 59.428 50.000 0.00 0.00 0.00 3.21
2134 2205 4.516698 GTGAATGTGTGTCTGATTGAGGTT 59.483 41.667 0.00 0.00 0.00 3.50
2135 2206 4.516321 TGAATGTGTGTCTGATTGAGGTTG 59.484 41.667 0.00 0.00 0.00 3.77
2136 2207 3.836365 TGTGTGTCTGATTGAGGTTGA 57.164 42.857 0.00 0.00 0.00 3.18
2137 2208 3.732212 TGTGTGTCTGATTGAGGTTGAG 58.268 45.455 0.00 0.00 0.00 3.02
2138 2209 3.070018 GTGTGTCTGATTGAGGTTGAGG 58.930 50.000 0.00 0.00 0.00 3.86
2139 2210 2.079925 GTGTCTGATTGAGGTTGAGGC 58.920 52.381 0.00 0.00 0.00 4.70
2175 2255 2.909006 TCTCTTCTGTTCCATTGGAGCT 59.091 45.455 18.85 0.00 33.98 4.09
2177 2257 3.679389 TCTTCTGTTCCATTGGAGCTTC 58.321 45.455 18.85 6.69 33.98 3.86
2184 2264 0.169672 CCATTGGAGCTTCTTGTGCG 59.830 55.000 0.00 0.00 35.28 5.34
2262 2342 0.698818 AGGTCCTGATGGGGAAACAC 59.301 55.000 0.00 0.00 37.10 3.32
2323 2409 1.610522 CCTTTCCCGATCAATCATGCC 59.389 52.381 0.00 0.00 0.00 4.40
2352 2438 1.484240 CAGGGGAACTCCAGCTAAGAG 59.516 57.143 10.63 10.63 37.91 2.85
2353 2439 1.362932 AGGGGAACTCCAGCTAAGAGA 59.637 52.381 17.50 0.00 37.91 3.10
2354 2440 2.188817 GGGGAACTCCAGCTAAGAGAA 58.811 52.381 17.50 0.00 37.91 2.87
2355 2441 2.169561 GGGGAACTCCAGCTAAGAGAAG 59.830 54.545 17.50 0.00 37.91 2.85
2356 2442 2.835156 GGGAACTCCAGCTAAGAGAAGT 59.165 50.000 17.50 4.66 37.91 3.01
2357 2443 4.024670 GGGAACTCCAGCTAAGAGAAGTA 58.975 47.826 17.50 0.00 37.91 2.24
2358 2444 4.098807 GGGAACTCCAGCTAAGAGAAGTAG 59.901 50.000 17.50 0.00 37.91 2.57
2359 2445 4.951094 GGAACTCCAGCTAAGAGAAGTAGA 59.049 45.833 17.50 0.00 35.27 2.59
2390 2476 4.167697 TCCCTCCTAACTCCTAACTCCTAC 59.832 50.000 0.00 0.00 0.00 3.18
2391 2477 4.168479 CCCTCCTAACTCCTAACTCCTACT 59.832 50.000 0.00 0.00 0.00 2.57
2392 2478 5.379187 CCTCCTAACTCCTAACTCCTACTC 58.621 50.000 0.00 0.00 0.00 2.59
2393 2479 5.033589 TCCTAACTCCTAACTCCTACTCG 57.966 47.826 0.00 0.00 0.00 4.18
2394 2480 4.472833 TCCTAACTCCTAACTCCTACTCGT 59.527 45.833 0.00 0.00 0.00 4.18
2395 2481 5.663106 TCCTAACTCCTAACTCCTACTCGTA 59.337 44.000 0.00 0.00 0.00 3.43
2406 2492 5.540911 ACTCCTACTCGTATCTAGCAGTAC 58.459 45.833 0.00 0.00 0.00 2.73
2407 2493 5.305128 ACTCCTACTCGTATCTAGCAGTACT 59.695 44.000 0.00 0.00 0.00 2.73
2434 2520 3.196685 ACTCTACACTGCCTCTGATTTCC 59.803 47.826 0.00 0.00 0.00 3.13
2457 2543 5.814705 CCTTGTTATCATCTTCCACTCACTC 59.185 44.000 0.00 0.00 0.00 3.51
2480 2566 2.754946 TTGACCGGCCTAACTAACAG 57.245 50.000 0.00 0.00 0.00 3.16
2542 2628 1.679032 GCAGGTATGGACAAGGACACC 60.679 57.143 0.00 0.00 0.00 4.16
2548 2634 4.202264 GGTATGGACAAGGACACCAGATAG 60.202 50.000 0.00 0.00 37.12 2.08
2549 2635 2.187958 TGGACAAGGACACCAGATAGG 58.812 52.381 0.00 0.00 45.67 2.57
2550 2636 2.225522 TGGACAAGGACACCAGATAGGA 60.226 50.000 0.00 0.00 41.22 2.94
2551 2637 2.432510 GGACAAGGACACCAGATAGGAG 59.567 54.545 0.00 0.00 41.22 3.69
2552 2638 1.834263 ACAAGGACACCAGATAGGAGC 59.166 52.381 0.00 0.00 41.22 4.70
2553 2639 1.833630 CAAGGACACCAGATAGGAGCA 59.166 52.381 0.00 0.00 41.22 4.26
2568 2657 4.927978 AGGAGCACTAGTACAATAGCTG 57.072 45.455 7.78 0.00 31.61 4.24
2569 2658 4.282496 AGGAGCACTAGTACAATAGCTGT 58.718 43.478 7.78 0.00 42.47 4.40
2570 2659 5.446860 AGGAGCACTAGTACAATAGCTGTA 58.553 41.667 7.78 0.00 39.64 2.74
2582 2671 9.947669 AGTACAATAGCTGTAGTATTTAACTCG 57.052 33.333 0.00 0.00 41.54 4.18
2597 2686 1.442769 ACTCGGCTGTGCTATTGTTG 58.557 50.000 0.00 0.00 0.00 3.33
2599 2688 1.394917 CTCGGCTGTGCTATTGTTGAC 59.605 52.381 0.00 0.00 0.00 3.18
2642 2731 3.119280 ACTGTTTTTCACCCAGGTTTTCG 60.119 43.478 0.00 0.00 0.00 3.46
2676 2765 2.193536 GGACCGTGCAGCTTTGGTT 61.194 57.895 5.43 0.00 34.12 3.67
2697 2786 1.683365 CCCCATGCCCAAGTTGAGG 60.683 63.158 3.87 5.24 0.00 3.86
2720 2809 4.489771 GGGATGTCCACTGGGCCG 62.490 72.222 0.00 0.00 37.91 6.13
2722 2811 2.746375 GGATGTCCACTGGGCCGAT 61.746 63.158 0.00 0.00 35.64 4.18
2726 2815 0.693622 TGTCCACTGGGCCGATTTTA 59.306 50.000 0.00 0.00 0.00 1.52
2727 2816 1.283613 TGTCCACTGGGCCGATTTTAT 59.716 47.619 0.00 0.00 0.00 1.40
2728 2817 2.291282 TGTCCACTGGGCCGATTTTATT 60.291 45.455 0.00 0.00 0.00 1.40
2733 2822 5.104444 TCCACTGGGCCGATTTTATTTAGTA 60.104 40.000 0.00 0.00 0.00 1.82
2734 2823 5.591067 CCACTGGGCCGATTTTATTTAGTAA 59.409 40.000 0.00 0.00 0.00 2.24
2736 2825 5.591472 ACTGGGCCGATTTTATTTAGTAACC 59.409 40.000 0.00 0.00 0.00 2.85
2754 2843 9.621629 TTAGTAACCAACAGATGAAAGAGAAAA 57.378 29.630 0.00 0.00 0.00 2.29
2755 2844 8.519799 AGTAACCAACAGATGAAAGAGAAAAA 57.480 30.769 0.00 0.00 0.00 1.94
2756 2845 8.624776 AGTAACCAACAGATGAAAGAGAAAAAG 58.375 33.333 0.00 0.00 0.00 2.27
2757 2846 6.396829 ACCAACAGATGAAAGAGAAAAAGG 57.603 37.500 0.00 0.00 0.00 3.11
2758 2847 5.221322 ACCAACAGATGAAAGAGAAAAAGGC 60.221 40.000 0.00 0.00 0.00 4.35
2759 2848 5.010415 CCAACAGATGAAAGAGAAAAAGGCT 59.990 40.000 0.00 0.00 0.00 4.58
2760 2849 6.207417 CCAACAGATGAAAGAGAAAAAGGCTA 59.793 38.462 0.00 0.00 0.00 3.93
2761 2850 6.809630 ACAGATGAAAGAGAAAAAGGCTAC 57.190 37.500 0.00 0.00 0.00 3.58
2762 2851 6.538263 ACAGATGAAAGAGAAAAAGGCTACT 58.462 36.000 0.00 0.00 0.00 2.57
2763 2852 7.680730 ACAGATGAAAGAGAAAAAGGCTACTA 58.319 34.615 0.00 0.00 0.00 1.82
2764 2853 7.604545 ACAGATGAAAGAGAAAAAGGCTACTAC 59.395 37.037 0.00 0.00 0.00 2.73
2765 2854 7.604164 CAGATGAAAGAGAAAAAGGCTACTACA 59.396 37.037 0.00 0.00 0.00 2.74
2766 2855 7.821846 AGATGAAAGAGAAAAAGGCTACTACAG 59.178 37.037 0.00 0.00 0.00 2.74
2767 2856 7.062749 TGAAAGAGAAAAAGGCTACTACAGA 57.937 36.000 0.00 0.00 0.00 3.41
2768 2857 7.680730 TGAAAGAGAAAAAGGCTACTACAGAT 58.319 34.615 0.00 0.00 0.00 2.90
2769 2858 7.819900 TGAAAGAGAAAAAGGCTACTACAGATC 59.180 37.037 0.00 0.00 0.00 2.75
2770 2859 6.859112 AGAGAAAAAGGCTACTACAGATCA 57.141 37.500 0.00 0.00 0.00 2.92
2771 2860 6.872920 AGAGAAAAAGGCTACTACAGATCAG 58.127 40.000 0.00 0.00 0.00 2.90
2772 2861 6.665680 AGAGAAAAAGGCTACTACAGATCAGA 59.334 38.462 0.00 0.00 0.00 3.27
2790 2879 9.636879 CAGATCAGATACTATGTTTCATACAGG 57.363 37.037 0.00 0.00 40.83 4.00
2792 2881 7.360113 TCAGATACTATGTTTCATACAGGCA 57.640 36.000 0.00 0.00 40.83 4.75
2795 2884 8.554528 CAGATACTATGTTTCATACAGGCAAAG 58.445 37.037 0.00 0.00 40.83 2.77
2802 2891 7.712264 TGTTTCATACAGGCAAAGAAAAATG 57.288 32.000 0.00 0.00 30.91 2.32
2803 2892 7.495901 TGTTTCATACAGGCAAAGAAAAATGA 58.504 30.769 0.00 0.00 30.91 2.57
2805 2894 8.490355 GTTTCATACAGGCAAAGAAAAATGAAG 58.510 33.333 0.00 0.00 34.60 3.02
2808 2897 4.768583 ACAGGCAAAGAAAAATGAAGCAA 58.231 34.783 0.00 0.00 0.00 3.91
2810 2899 5.824097 ACAGGCAAAGAAAAATGAAGCAAAT 59.176 32.000 0.00 0.00 0.00 2.32
2833 2922 7.726033 ATATAGGTTATACAGGGCTCAAGAG 57.274 40.000 0.00 0.00 0.00 2.85
2928 3017 9.136323 AGAAGTTGACAAAGTTTTATCCATTCT 57.864 29.630 0.00 0.00 0.00 2.40
2948 3037 0.685458 AATGCTCATGCCTTCCCCAC 60.685 55.000 0.00 0.00 38.71 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.976490 TACTGTCCTGGGGGCTCGG 62.976 68.421 0.00 0.00 0.00 4.63
14 15 1.987855 TTACTGTCCTGGGGGCTCG 60.988 63.158 0.00 0.00 0.00 5.03
15 16 1.602771 GTTACTGTCCTGGGGGCTC 59.397 63.158 0.00 0.00 0.00 4.70
16 17 1.923909 GGTTACTGTCCTGGGGGCT 60.924 63.158 0.00 0.00 0.00 5.19
17 18 2.675371 GGTTACTGTCCTGGGGGC 59.325 66.667 0.00 0.00 0.00 5.80
18 19 2.306384 GGGGTTACTGTCCTGGGGG 61.306 68.421 0.00 0.00 0.00 5.40
19 20 2.666098 CGGGGTTACTGTCCTGGGG 61.666 68.421 0.00 0.00 0.00 4.96
20 21 1.611261 TCGGGGTTACTGTCCTGGG 60.611 63.158 0.00 0.00 0.00 4.45
21 22 1.898154 CTCGGGGTTACTGTCCTGG 59.102 63.158 0.00 0.00 0.00 4.45
22 23 1.218316 GCTCGGGGTTACTGTCCTG 59.782 63.158 0.00 0.00 0.00 3.86
23 24 0.971447 GAGCTCGGGGTTACTGTCCT 60.971 60.000 0.00 0.00 0.00 3.85
24 25 1.255667 TGAGCTCGGGGTTACTGTCC 61.256 60.000 9.64 0.00 0.00 4.02
25 26 0.108756 GTGAGCTCGGGGTTACTGTC 60.109 60.000 9.64 0.00 0.00 3.51
26 27 1.542187 GGTGAGCTCGGGGTTACTGT 61.542 60.000 9.41 0.00 31.47 3.55
27 28 1.218316 GGTGAGCTCGGGGTTACTG 59.782 63.158 9.41 0.00 31.47 2.74
28 29 2.348888 CGGTGAGCTCGGGGTTACT 61.349 63.158 9.41 0.00 31.47 2.24
29 30 2.183555 CGGTGAGCTCGGGGTTAC 59.816 66.667 9.64 0.00 0.00 2.50
30 31 3.766691 GCGGTGAGCTCGGGGTTA 61.767 66.667 9.64 0.00 44.04 2.85
40 41 0.970937 TCAGGTAAGAGGGCGGTGAG 60.971 60.000 0.00 0.00 0.00 3.51
41 42 0.970937 CTCAGGTAAGAGGGCGGTGA 60.971 60.000 0.00 0.00 31.94 4.02
42 43 0.970937 TCTCAGGTAAGAGGGCGGTG 60.971 60.000 0.00 0.00 36.30 4.94
43 44 0.971447 GTCTCAGGTAAGAGGGCGGT 60.971 60.000 0.00 0.00 36.30 5.68
44 45 1.677637 GGTCTCAGGTAAGAGGGCGG 61.678 65.000 0.00 0.00 36.30 6.13
45 46 1.817209 GGTCTCAGGTAAGAGGGCG 59.183 63.158 0.00 0.00 36.30 6.13
46 47 0.683504 TCGGTCTCAGGTAAGAGGGC 60.684 60.000 0.00 0.00 36.30 5.19
47 48 1.064611 TCTCGGTCTCAGGTAAGAGGG 60.065 57.143 0.00 0.00 36.30 4.30
48 49 2.294074 CTCTCGGTCTCAGGTAAGAGG 58.706 57.143 0.00 0.00 36.30 3.69
49 50 1.673920 GCTCTCGGTCTCAGGTAAGAG 59.326 57.143 0.00 0.00 36.97 2.85
50 51 1.682394 GGCTCTCGGTCTCAGGTAAGA 60.682 57.143 0.00 0.00 0.00 2.10
51 52 0.741915 GGCTCTCGGTCTCAGGTAAG 59.258 60.000 0.00 0.00 0.00 2.34
52 53 0.039180 TGGCTCTCGGTCTCAGGTAA 59.961 55.000 0.00 0.00 0.00 2.85
53 54 0.259065 ATGGCTCTCGGTCTCAGGTA 59.741 55.000 0.00 0.00 0.00 3.08
54 55 1.000993 ATGGCTCTCGGTCTCAGGT 59.999 57.895 0.00 0.00 0.00 4.00
55 56 1.739049 GATGGCTCTCGGTCTCAGG 59.261 63.158 0.00 0.00 0.00 3.86
56 57 1.358402 CGATGGCTCTCGGTCTCAG 59.642 63.158 2.69 0.00 35.03 3.35
57 58 3.514417 CGATGGCTCTCGGTCTCA 58.486 61.111 2.69 0.00 35.03 3.27
85 86 4.148825 ACGACGAGAGGCCATGGC 62.149 66.667 29.47 29.47 41.06 4.40
86 87 2.105128 GACGACGAGAGGCCATGG 59.895 66.667 7.63 7.63 33.32 3.66
87 88 2.278206 CGACGACGAGAGGCCATG 60.278 66.667 5.01 0.00 42.66 3.66
88 89 2.437895 TCGACGACGAGAGGCCAT 60.438 61.111 5.01 0.00 43.81 4.40
97 98 1.329599 TCACCATGAGTATCGACGACG 59.670 52.381 0.00 0.00 38.61 5.12
98 99 3.416119 TTCACCATGAGTATCGACGAC 57.584 47.619 0.00 0.00 38.61 4.34
99 100 3.442625 AGTTTCACCATGAGTATCGACGA 59.557 43.478 0.00 0.00 38.61 4.20
100 101 3.770666 AGTTTCACCATGAGTATCGACG 58.229 45.455 0.00 0.00 38.61 5.12
101 102 4.330074 CCAAGTTTCACCATGAGTATCGAC 59.670 45.833 0.00 0.00 38.61 4.20
102 103 4.503910 CCAAGTTTCACCATGAGTATCGA 58.496 43.478 0.00 0.00 38.61 3.59
103 104 3.623060 CCCAAGTTTCACCATGAGTATCG 59.377 47.826 0.00 0.00 38.61 2.92
104 105 4.843728 TCCCAAGTTTCACCATGAGTATC 58.156 43.478 0.00 0.00 0.00 2.24
105 106 4.848357 CTCCCAAGTTTCACCATGAGTAT 58.152 43.478 0.00 0.00 0.00 2.12
106 107 3.559171 GCTCCCAAGTTTCACCATGAGTA 60.559 47.826 0.00 0.00 0.00 2.59
107 108 2.815589 GCTCCCAAGTTTCACCATGAGT 60.816 50.000 0.00 0.00 0.00 3.41
108 109 1.815003 GCTCCCAAGTTTCACCATGAG 59.185 52.381 0.00 0.00 0.00 2.90
109 110 1.881925 CGCTCCCAAGTTTCACCATGA 60.882 52.381 0.00 0.00 0.00 3.07
110 111 0.523072 CGCTCCCAAGTTTCACCATG 59.477 55.000 0.00 0.00 0.00 3.66
111 112 0.110486 ACGCTCCCAAGTTTCACCAT 59.890 50.000 0.00 0.00 0.00 3.55
112 113 0.759959 TACGCTCCCAAGTTTCACCA 59.240 50.000 0.00 0.00 0.00 4.17
113 114 1.270678 ACTACGCTCCCAAGTTTCACC 60.271 52.381 0.00 0.00 0.00 4.02
114 115 2.165319 ACTACGCTCCCAAGTTTCAC 57.835 50.000 0.00 0.00 0.00 3.18
115 116 3.159472 TCTACTACGCTCCCAAGTTTCA 58.841 45.455 0.00 0.00 0.00 2.69
116 117 3.863142 TCTACTACGCTCCCAAGTTTC 57.137 47.619 0.00 0.00 0.00 2.78
117 118 4.612264 TTTCTACTACGCTCCCAAGTTT 57.388 40.909 0.00 0.00 0.00 2.66
118 119 4.612264 TTTTCTACTACGCTCCCAAGTT 57.388 40.909 0.00 0.00 0.00 2.66
119 120 4.313282 GTTTTTCTACTACGCTCCCAAGT 58.687 43.478 0.00 0.00 0.00 3.16
120 121 3.367025 CGTTTTTCTACTACGCTCCCAAG 59.633 47.826 0.00 0.00 0.00 3.61
121 122 3.319755 CGTTTTTCTACTACGCTCCCAA 58.680 45.455 0.00 0.00 0.00 4.12
122 123 2.353011 CCGTTTTTCTACTACGCTCCCA 60.353 50.000 0.00 0.00 34.16 4.37
123 124 2.094545 TCCGTTTTTCTACTACGCTCCC 60.095 50.000 0.00 0.00 34.16 4.30
124 125 3.221964 TCCGTTTTTCTACTACGCTCC 57.778 47.619 0.00 0.00 34.16 4.70
125 126 5.580911 TTTTCCGTTTTTCTACTACGCTC 57.419 39.130 0.00 0.00 34.16 5.03
126 127 7.838771 ATATTTTCCGTTTTTCTACTACGCT 57.161 32.000 0.00 0.00 34.16 5.07
127 128 9.577003 CATATATTTTCCGTTTTTCTACTACGC 57.423 33.333 0.00 0.00 34.16 4.42
141 142 3.935203 AGGAGCATCGCATATATTTTCCG 59.065 43.478 0.00 0.00 34.37 4.30
153 154 1.214062 CCGATCCTAGGAGCATCGC 59.786 63.158 25.98 6.22 34.37 4.58
170 173 1.069358 GCCACTACACTATGCTCCTCC 59.931 57.143 0.00 0.00 0.00 4.30
171 174 1.069358 GGCCACTACACTATGCTCCTC 59.931 57.143 0.00 0.00 0.00 3.71
172 175 1.123928 GGCCACTACACTATGCTCCT 58.876 55.000 0.00 0.00 0.00 3.69
244 247 1.761244 TAAATGCGTGCGCCATCTCG 61.761 55.000 14.16 3.23 41.09 4.04
245 248 0.316196 GTAAATGCGTGCGCCATCTC 60.316 55.000 14.16 0.00 41.09 2.75
282 285 2.621371 CTTTCTCCCTCCGCTCGCTC 62.621 65.000 0.00 0.00 0.00 5.03
284 287 2.202810 CTTTCTCCCTCCGCTCGC 60.203 66.667 0.00 0.00 0.00 5.03
285 288 0.179124 CTTCTTTCTCCCTCCGCTCG 60.179 60.000 0.00 0.00 0.00 5.03
287 290 0.545548 ACCTTCTTTCTCCCTCCGCT 60.546 55.000 0.00 0.00 0.00 5.52
288 291 0.325272 AACCTTCTTTCTCCCTCCGC 59.675 55.000 0.00 0.00 0.00 5.54
289 292 1.066071 GGAACCTTCTTTCTCCCTCCG 60.066 57.143 0.00 0.00 0.00 4.63
290 293 2.791347 GGAACCTTCTTTCTCCCTCC 57.209 55.000 0.00 0.00 0.00 4.30
310 335 1.726672 GGCGTGGCGTTTTAAACCG 60.727 57.895 0.15 0.15 0.00 4.44
414 439 2.807107 CGCTGGCTGGCTATGGGTA 61.807 63.158 2.00 0.00 0.00 3.69
416 441 4.181010 ACGCTGGCTGGCTATGGG 62.181 66.667 2.00 4.16 0.00 4.00
420 445 3.461773 GGAGACGCTGGCTGGCTA 61.462 66.667 2.00 0.00 0.00 3.93
793 818 0.103208 ATGATGACGGAGCTCGGTTC 59.897 55.000 25.61 20.09 44.45 3.62
857 882 1.972752 TATACATAGGCGGCGGCGA 60.973 57.895 36.87 23.80 41.24 5.54
876 901 1.967779 GCTAAGGAGGAGGAAGGCTAG 59.032 57.143 0.00 0.00 0.00 3.42
887 912 3.560882 GGATGAATGATGGGCTAAGGAGG 60.561 52.174 0.00 0.00 0.00 4.30
888 913 3.073503 TGGATGAATGATGGGCTAAGGAG 59.926 47.826 0.00 0.00 0.00 3.69
889 914 3.055328 TGGATGAATGATGGGCTAAGGA 58.945 45.455 0.00 0.00 0.00 3.36
890 915 3.513909 TGGATGAATGATGGGCTAAGG 57.486 47.619 0.00 0.00 0.00 2.69
891 916 4.015084 GGATGGATGAATGATGGGCTAAG 58.985 47.826 0.00 0.00 0.00 2.18
892 917 3.245371 GGGATGGATGAATGATGGGCTAA 60.245 47.826 0.00 0.00 0.00 3.09
893 918 2.309755 GGGATGGATGAATGATGGGCTA 59.690 50.000 0.00 0.00 0.00 3.93
894 919 1.076677 GGGATGGATGAATGATGGGCT 59.923 52.381 0.00 0.00 0.00 5.19
895 920 1.553706 GGGATGGATGAATGATGGGC 58.446 55.000 0.00 0.00 0.00 5.36
896 921 1.615116 CGGGGATGGATGAATGATGGG 60.615 57.143 0.00 0.00 0.00 4.00
897 922 1.352017 TCGGGGATGGATGAATGATGG 59.648 52.381 0.00 0.00 0.00 3.51
916 946 0.096281 CGACGAGCTGAGAGACACTC 59.904 60.000 0.00 0.00 45.11 3.51
917 947 1.302383 CCGACGAGCTGAGAGACACT 61.302 60.000 0.00 0.00 0.00 3.55
929 959 1.280142 CCTATGACGAGCCGACGAG 59.720 63.158 0.00 0.00 37.03 4.18
936 966 1.339610 AGTGATGAGCCTATGACGAGC 59.660 52.381 0.00 0.00 0.00 5.03
937 967 3.818210 ACTAGTGATGAGCCTATGACGAG 59.182 47.826 0.00 0.00 0.00 4.18
938 968 3.565902 CACTAGTGATGAGCCTATGACGA 59.434 47.826 18.45 0.00 0.00 4.20
940 970 3.891977 TCCACTAGTGATGAGCCTATGAC 59.108 47.826 24.68 0.00 0.00 3.06
941 971 4.184649 TCCACTAGTGATGAGCCTATGA 57.815 45.455 24.68 5.78 0.00 2.15
942 972 5.126869 CCTATCCACTAGTGATGAGCCTATG 59.873 48.000 24.68 3.36 0.00 2.23
943 973 5.268387 CCTATCCACTAGTGATGAGCCTAT 58.732 45.833 24.68 6.77 0.00 2.57
944 974 4.667573 CCTATCCACTAGTGATGAGCCTA 58.332 47.826 24.68 3.17 0.00 3.93
945 975 3.505386 CCTATCCACTAGTGATGAGCCT 58.495 50.000 24.68 2.14 0.00 4.58
946 976 2.028567 GCCTATCCACTAGTGATGAGCC 60.029 54.545 24.68 3.97 0.00 4.70
947 977 2.352225 CGCCTATCCACTAGTGATGAGC 60.352 54.545 24.68 17.17 0.00 4.26
948 978 2.352225 GCGCCTATCCACTAGTGATGAG 60.352 54.545 24.68 15.80 0.00 2.90
949 979 1.613925 GCGCCTATCCACTAGTGATGA 59.386 52.381 24.68 13.93 0.00 2.92
950 980 1.337260 GGCGCCTATCCACTAGTGATG 60.337 57.143 24.68 8.61 0.00 3.07
951 981 0.969894 GGCGCCTATCCACTAGTGAT 59.030 55.000 24.68 16.61 0.00 3.06
952 982 0.106167 AGGCGCCTATCCACTAGTGA 60.106 55.000 31.86 10.67 0.00 3.41
953 983 0.753262 AAGGCGCCTATCCACTAGTG 59.247 55.000 33.07 16.34 0.00 2.74
954 984 0.753262 CAAGGCGCCTATCCACTAGT 59.247 55.000 33.07 7.71 0.00 2.57
955 985 0.034059 CCAAGGCGCCTATCCACTAG 59.966 60.000 33.07 11.79 0.00 2.57
956 986 0.689745 ACCAAGGCGCCTATCCACTA 60.690 55.000 33.07 0.00 0.00 2.74
957 987 1.972660 GACCAAGGCGCCTATCCACT 61.973 60.000 33.07 10.49 0.00 4.00
958 988 1.523938 GACCAAGGCGCCTATCCAC 60.524 63.158 33.07 16.51 0.00 4.02
959 989 2.908015 GACCAAGGCGCCTATCCA 59.092 61.111 33.07 0.00 0.00 3.41
960 990 2.280186 CGACCAAGGCGCCTATCC 60.280 66.667 33.07 17.91 0.00 2.59
961 991 1.300233 CTCGACCAAGGCGCCTATC 60.300 63.158 33.07 25.19 0.00 2.08
962 992 2.017559 GACTCGACCAAGGCGCCTAT 62.018 60.000 33.07 19.14 0.00 2.57
963 993 2.678934 ACTCGACCAAGGCGCCTA 60.679 61.111 33.07 12.47 0.00 3.93
964 994 4.070552 GACTCGACCAAGGCGCCT 62.071 66.667 27.08 27.08 0.00 5.52
968 998 3.692406 ACCCGACTCGACCAAGGC 61.692 66.667 0.00 0.00 0.00 4.35
969 999 2.214181 CTCACCCGACTCGACCAAGG 62.214 65.000 0.00 0.00 0.00 3.61
970 1000 1.213013 CTCACCCGACTCGACCAAG 59.787 63.158 0.00 0.00 0.00 3.61
971 1001 2.273179 CCTCACCCGACTCGACCAA 61.273 63.158 0.00 0.00 0.00 3.67
972 1002 2.675423 CCTCACCCGACTCGACCA 60.675 66.667 0.00 0.00 0.00 4.02
973 1003 3.450115 CCCTCACCCGACTCGACC 61.450 72.222 0.00 0.00 0.00 4.79
974 1004 3.450115 CCCCTCACCCGACTCGAC 61.450 72.222 0.00 0.00 0.00 4.20
977 1007 3.775654 CTGCCCCTCACCCGACTC 61.776 72.222 0.00 0.00 0.00 3.36
1158 1188 2.111043 AGGTTCCTGCACCACGTG 59.889 61.111 9.08 9.08 39.62 4.49
1960 2020 3.203487 AGGGTGTCTAGCTAGCTAAGTCT 59.797 47.826 24.20 13.01 0.00 3.24
1961 2021 3.316868 CAGGGTGTCTAGCTAGCTAAGTC 59.683 52.174 24.20 16.75 0.00 3.01
1962 2022 3.292460 CAGGGTGTCTAGCTAGCTAAGT 58.708 50.000 24.20 2.49 0.00 2.24
1963 2023 2.035321 GCAGGGTGTCTAGCTAGCTAAG 59.965 54.545 24.20 17.55 0.00 2.18
1964 2024 2.032620 GCAGGGTGTCTAGCTAGCTAA 58.967 52.381 24.20 13.01 0.00 3.09
1977 2047 1.468520 CAAACGAATGTAGGCAGGGTG 59.531 52.381 0.00 0.00 0.00 4.61
1978 2048 1.073284 ACAAACGAATGTAGGCAGGGT 59.927 47.619 0.00 0.00 0.00 4.34
1980 2050 4.000988 AGTAACAAACGAATGTAGGCAGG 58.999 43.478 0.00 0.00 32.02 4.85
1983 2053 3.425758 GGCAGTAACAAACGAATGTAGGC 60.426 47.826 0.00 0.00 32.02 3.93
2023 2094 4.643334 ACATGGTGAAATGTCCATCATCAG 59.357 41.667 0.00 0.00 39.83 2.90
2049 2120 4.433615 ACATGGTAGAAGTATGTTGCTCG 58.566 43.478 0.00 0.00 31.38 5.03
2062 2133 9.955208 CGTTACATACTTACATTACATGGTAGA 57.045 33.333 0.00 0.00 33.60 2.59
2079 2150 7.025365 TCTTACACTCACACATCGTTACATAC 58.975 38.462 0.00 0.00 0.00 2.39
2080 2151 7.148355 TCTTACACTCACACATCGTTACATA 57.852 36.000 0.00 0.00 0.00 2.29
2085 2156 3.306088 CCCTCTTACACTCACACATCGTT 60.306 47.826 0.00 0.00 0.00 3.85
2086 2157 2.231478 CCCTCTTACACTCACACATCGT 59.769 50.000 0.00 0.00 0.00 3.73
2087 2158 2.417379 CCCCTCTTACACTCACACATCG 60.417 54.545 0.00 0.00 0.00 3.84
2088 2159 2.093447 CCCCCTCTTACACTCACACATC 60.093 54.545 0.00 0.00 0.00 3.06
2089 2160 1.909302 CCCCCTCTTACACTCACACAT 59.091 52.381 0.00 0.00 0.00 3.21
2090 2161 1.132977 TCCCCCTCTTACACTCACACA 60.133 52.381 0.00 0.00 0.00 3.72
2091 2162 1.550976 CTCCCCCTCTTACACTCACAC 59.449 57.143 0.00 0.00 0.00 3.82
2092 2163 1.149288 ACTCCCCCTCTTACACTCACA 59.851 52.381 0.00 0.00 0.00 3.58
2093 2164 1.550976 CACTCCCCCTCTTACACTCAC 59.449 57.143 0.00 0.00 0.00 3.51
2094 2165 1.431633 TCACTCCCCCTCTTACACTCA 59.568 52.381 0.00 0.00 0.00 3.41
2119 2190 2.079925 GCCTCAACCTCAATCAGACAC 58.920 52.381 0.00 0.00 0.00 3.67
2184 2264 2.182842 GCCGATCCTCCATGTGCAC 61.183 63.158 10.75 10.75 0.00 4.57
2218 2298 3.155167 CCTCGCCCCCAGGACTAC 61.155 72.222 0.00 0.00 31.91 2.73
2243 2323 0.698818 GTGTTTCCCCATCAGGACCT 59.301 55.000 0.00 0.00 38.24 3.85
2311 2397 3.820467 TGGATAAACCGGCATGATTGATC 59.180 43.478 0.00 0.00 42.61 2.92
2323 2409 1.134189 GGAGTTCCCCTGGATAAACCG 60.134 57.143 0.00 0.00 42.61 4.44
2352 2438 2.761767 GGAGGGACCAGTTCTCTACTTC 59.238 54.545 0.00 0.00 33.85 3.01
2353 2439 2.384029 AGGAGGGACCAGTTCTCTACTT 59.616 50.000 0.00 0.00 44.97 2.24
2354 2440 2.004589 AGGAGGGACCAGTTCTCTACT 58.995 52.381 0.00 0.00 41.99 2.57
2355 2441 2.535836 AGGAGGGACCAGTTCTCTAC 57.464 55.000 0.00 0.00 33.85 2.59
2356 2442 3.596956 AGTTAGGAGGGACCAGTTCTCTA 59.403 47.826 0.00 0.00 33.85 2.43
2357 2443 2.384029 AGTTAGGAGGGACCAGTTCTCT 59.616 50.000 0.00 0.00 38.01 3.10
2358 2444 2.761767 GAGTTAGGAGGGACCAGTTCTC 59.238 54.545 0.00 0.00 42.04 2.87
2359 2445 2.560158 GGAGTTAGGAGGGACCAGTTCT 60.560 54.545 0.00 0.00 42.04 3.01
2390 2476 6.684686 AGTAGAGAGTACTGCTAGATACGAG 58.315 44.000 0.00 0.00 31.59 4.18
2391 2477 6.491062 AGAGTAGAGAGTACTGCTAGATACGA 59.509 42.308 0.00 0.00 33.37 3.43
2392 2478 6.684686 AGAGTAGAGAGTACTGCTAGATACG 58.315 44.000 0.00 0.00 33.37 3.06
2393 2479 8.579006 TGTAGAGTAGAGAGTACTGCTAGATAC 58.421 40.741 0.00 6.03 33.37 2.24
2394 2480 8.579006 GTGTAGAGTAGAGAGTACTGCTAGATA 58.421 40.741 0.00 0.00 33.37 1.98
2395 2481 7.289317 AGTGTAGAGTAGAGAGTACTGCTAGAT 59.711 40.741 0.00 0.00 33.37 1.98
2406 2492 3.876914 CAGAGGCAGTGTAGAGTAGAGAG 59.123 52.174 0.00 0.00 0.00 3.20
2407 2493 3.519913 TCAGAGGCAGTGTAGAGTAGAGA 59.480 47.826 0.00 0.00 0.00 3.10
2434 2520 6.312426 GTGAGTGAGTGGAAGATGATAACAAG 59.688 42.308 0.00 0.00 0.00 3.16
2457 2543 2.740447 GTTAGTTAGGCCGGTCAAAGTG 59.260 50.000 9.71 0.00 0.00 3.16
2480 2566 3.198853 AGGAAAGCAGAGGGATGTTAGTC 59.801 47.826 0.00 0.00 0.00 2.59
2542 2628 6.432783 AGCTATTGTACTAGTGCTCCTATCTG 59.567 42.308 12.42 0.00 0.00 2.90
2548 2634 4.657436 ACAGCTATTGTACTAGTGCTCC 57.343 45.455 12.42 0.00 38.56 4.70
2549 2635 6.380095 ACTACAGCTATTGTACTAGTGCTC 57.620 41.667 12.42 0.58 41.29 4.26
2550 2636 8.466617 AATACTACAGCTATTGTACTAGTGCT 57.533 34.615 12.42 4.96 41.29 4.40
2568 2657 4.430908 AGCACAGCCGAGTTAAATACTAC 58.569 43.478 0.00 0.00 37.17 2.73
2569 2658 4.730949 AGCACAGCCGAGTTAAATACTA 57.269 40.909 0.00 0.00 37.17 1.82
2570 2659 3.611766 AGCACAGCCGAGTTAAATACT 57.388 42.857 0.00 0.00 40.71 2.12
2582 2671 0.447801 CCGTCAACAATAGCACAGCC 59.552 55.000 0.00 0.00 0.00 4.85
2597 2686 1.006571 TCTTTGACCAGTCGCCGTC 60.007 57.895 0.00 0.00 0.00 4.79
2599 2688 1.006102 ACTCTTTGACCAGTCGCCG 60.006 57.895 0.00 0.00 0.00 6.46
2663 2752 0.817654 GGGGATAACCAAAGCTGCAC 59.182 55.000 1.02 0.00 42.91 4.57
2676 2765 1.215173 CTCAACTTGGGCATGGGGATA 59.785 52.381 0.00 0.00 0.00 2.59
2697 2786 0.035056 CCAGTGGACATCCCTGAACC 60.035 60.000 1.68 0.00 36.83 3.62
2698 2787 0.035056 CCCAGTGGACATCCCTGAAC 60.035 60.000 11.95 0.00 36.83 3.18
2699 2788 1.852157 GCCCAGTGGACATCCCTGAA 61.852 60.000 11.95 0.00 36.83 3.02
2726 2815 9.793259 TTCTCTTTCATCTGTTGGTTACTAAAT 57.207 29.630 0.00 0.00 0.00 1.40
2727 2816 9.621629 TTTCTCTTTCATCTGTTGGTTACTAAA 57.378 29.630 0.00 0.00 0.00 1.85
2728 2817 9.621629 TTTTCTCTTTCATCTGTTGGTTACTAA 57.378 29.630 0.00 0.00 0.00 2.24
2733 2822 6.683861 GCCTTTTTCTCTTTCATCTGTTGGTT 60.684 38.462 0.00 0.00 0.00 3.67
2734 2823 5.221322 GCCTTTTTCTCTTTCATCTGTTGGT 60.221 40.000 0.00 0.00 0.00 3.67
2736 2825 6.081872 AGCCTTTTTCTCTTTCATCTGTTG 57.918 37.500 0.00 0.00 0.00 3.33
2745 2834 7.680730 TGATCTGTAGTAGCCTTTTTCTCTTT 58.319 34.615 0.00 0.00 0.00 2.52
2747 2836 6.665680 TCTGATCTGTAGTAGCCTTTTTCTCT 59.334 38.462 0.00 0.00 0.00 3.10
2748 2837 6.868622 TCTGATCTGTAGTAGCCTTTTTCTC 58.131 40.000 0.00 0.00 0.00 2.87
2749 2838 6.859112 TCTGATCTGTAGTAGCCTTTTTCT 57.141 37.500 0.00 0.00 0.00 2.52
2754 2843 8.167392 ACATAGTATCTGATCTGTAGTAGCCTT 58.833 37.037 0.00 0.00 0.00 4.35
2755 2844 7.695055 ACATAGTATCTGATCTGTAGTAGCCT 58.305 38.462 0.00 0.00 0.00 4.58
2756 2845 7.931578 ACATAGTATCTGATCTGTAGTAGCC 57.068 40.000 0.00 0.00 0.00 3.93
2757 2846 9.834628 GAAACATAGTATCTGATCTGTAGTAGC 57.165 37.037 0.00 0.00 0.00 3.58
2764 2853 9.636879 CCTGTATGAAACATAGTATCTGATCTG 57.363 37.037 0.00 0.00 37.50 2.90
2765 2854 8.310382 GCCTGTATGAAACATAGTATCTGATCT 58.690 37.037 0.00 0.00 37.50 2.75
2766 2855 8.090831 TGCCTGTATGAAACATAGTATCTGATC 58.909 37.037 0.00 0.00 37.50 2.92
2767 2856 7.966812 TGCCTGTATGAAACATAGTATCTGAT 58.033 34.615 0.00 0.00 37.50 2.90
2768 2857 7.360113 TGCCTGTATGAAACATAGTATCTGA 57.640 36.000 0.00 0.00 37.50 3.27
2769 2858 8.437360 TTTGCCTGTATGAAACATAGTATCTG 57.563 34.615 0.00 0.00 37.50 2.90
2770 2859 8.486210 TCTTTGCCTGTATGAAACATAGTATCT 58.514 33.333 0.00 0.00 37.50 1.98
2771 2860 8.662781 TCTTTGCCTGTATGAAACATAGTATC 57.337 34.615 0.00 0.00 37.50 2.24
2772 2861 9.461312 TTTCTTTGCCTGTATGAAACATAGTAT 57.539 29.630 0.00 0.00 37.50 2.12
2790 2879 9.154847 ACCTATATTTGCTTCATTTTTCTTTGC 57.845 29.630 0.00 0.00 0.00 3.68
2802 2891 7.168905 AGCCCTGTATAACCTATATTTGCTTC 58.831 38.462 0.00 0.00 0.00 3.86
2803 2892 7.091533 AGCCCTGTATAACCTATATTTGCTT 57.908 36.000 0.00 0.00 0.00 3.91
2805 2894 6.472887 TGAGCCCTGTATAACCTATATTTGC 58.527 40.000 0.00 0.00 0.00 3.68
2808 2897 7.956315 TCTCTTGAGCCCTGTATAACCTATATT 59.044 37.037 0.00 0.00 0.00 1.28
2810 2899 6.860034 TCTCTTGAGCCCTGTATAACCTATA 58.140 40.000 0.00 0.00 0.00 1.31
2833 2922 5.639931 CAGGGAGCTACTGTACTTTCTTTTC 59.360 44.000 9.22 0.00 0.00 2.29
2928 3017 0.925558 TGGGGAAGGCATGAGCATTA 59.074 50.000 0.00 0.00 45.98 1.90


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

AutoCloner maintained by Alex Coulton.