Multiple sequence alignment - TraesCS7B01G227900

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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 TraesCS7B01G227900 chr7B 100.000 4462 0 0 1 4462 428092352 428096813 0.000000e+00 8240.0
1 TraesCS7B01G227900 chr7D 91.239 3607 191 53 874 4403 413690457 413694015 0.000000e+00 4795.0
2 TraesCS7B01G227900 chr7D 92.898 704 31 6 185 876 413689713 413690409 0.000000e+00 1005.0
3 TraesCS7B01G227900 chr7D 91.333 150 11 2 1537 1686 40412524 40412377 2.100000e-48 204.0
4 TraesCS7B01G227900 chr7D 100.000 29 0 0 168 196 413687517 413687545 2.000000e-03 54.7
5 TraesCS7B01G227900 chr7D 100.000 28 0 0 168 195 413682168 413682195 8.000000e-03 52.8
6 TraesCS7B01G227900 chr7A 91.326 2859 174 37 875 3683 475771277 475774111 0.000000e+00 3838.0
7 TraesCS7B01G227900 chr7A 90.000 580 39 5 187 753 475770465 475771038 0.000000e+00 732.0
8 TraesCS7B01G227900 chr7A 88.477 486 32 9 3983 4446 475774999 475775482 2.330000e-157 566.0
9 TraesCS7B01G227900 chr4D 78.261 184 40 0 3168 3351 468422117 468422300 7.840000e-23 119.0


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 TraesCS7B01G227900 chr7B 428092352 428096813 4461 False 8240.000000 8240 100.000000 1 4462 1 chr7B.!!$F1 4461
1 TraesCS7B01G227900 chr7D 413687517 413694015 6498 False 1951.566667 4795 94.712333 168 4403 3 chr7D.!!$F2 4235
2 TraesCS7B01G227900 chr7A 475770465 475775482 5017 False 1712.000000 3838 89.934333 187 4446 3 chr7A.!!$F1 4259

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
54 55 0.027586 GCGGATTAACCATGTCACGC 59.972 55.0 0.00 0.0 38.90 5.34 F
59 60 0.036164 TTAACCATGTCACGCCTGCT 59.964 50.0 0.00 0.0 0.00 4.24 F
77 78 0.036732 CTGCACCAAGCTGTCCCTAA 59.963 55.0 0.00 0.0 45.94 2.69 F
117 118 0.109412 CGCGAACTTCCTTACGGTCT 60.109 55.0 0.00 0.0 0.00 3.85 F
126 127 0.463833 CCTTACGGTCTTCATGGCCC 60.464 60.0 0.00 0.0 37.05 5.80 F
1261 3590 0.595053 ATATCTGCTCACGCGTTCCG 60.595 55.0 10.22 0.0 44.21 4.30 F
2448 4814 0.389948 CTGGGACTGTCTGTAACGCC 60.390 60.0 7.85 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1897 4246 0.539986 ATGTGTAGCTGGTTACCCCG 59.460 55.000 0.00 0.00 35.15 5.73 R
1988 4353 2.097825 GAACTCCAGCTTCCGTACCTA 58.902 52.381 0.00 0.00 0.00 3.08 R
2008 4373 3.289834 ACCAGCAGCGCAACCAAG 61.290 61.111 11.47 0.00 0.00 3.61 R
2180 4545 6.572119 TGGCAAATGGCAGTTAAATTCTGTAG 60.572 38.462 5.46 0.00 46.12 2.74 R
2224 4590 2.014857 CACATGTAAGATGCAGCAGCT 58.985 47.619 7.55 7.55 42.74 4.24 R
2933 5299 0.937304 CTTGCATGGACGATAACCCG 59.063 55.000 0.00 0.00 0.00 5.28 R
4391 7385 0.040067 GTGCTTGCCAAAACCTCGAG 60.040 55.000 5.13 5.13 0.00 4.04 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
32 33 8.798859 ATTAATGATTGTGATATACAGCTCCC 57.201 34.615 0.00 0.00 41.10 4.30
33 34 4.623932 TGATTGTGATATACAGCTCCCC 57.376 45.455 0.00 0.00 41.10 4.81
34 35 4.234550 TGATTGTGATATACAGCTCCCCT 58.765 43.478 0.00 0.00 41.10 4.79
36 37 1.694150 TGTGATATACAGCTCCCCTGC 59.306 52.381 0.00 0.00 45.78 4.85
37 38 0.969149 TGATATACAGCTCCCCTGCG 59.031 55.000 0.00 0.00 45.78 5.18
38 39 0.247736 GATATACAGCTCCCCTGCGG 59.752 60.000 0.00 0.00 45.78 5.69
39 40 0.178932 ATATACAGCTCCCCTGCGGA 60.179 55.000 0.00 0.00 45.78 5.54
40 41 0.178932 TATACAGCTCCCCTGCGGAT 60.179 55.000 0.00 0.00 45.78 4.18
41 42 1.056700 ATACAGCTCCCCTGCGGATT 61.057 55.000 0.00 0.00 45.78 3.01
42 43 0.397957 TACAGCTCCCCTGCGGATTA 60.398 55.000 0.00 0.00 45.78 1.75
43 44 1.271840 ACAGCTCCCCTGCGGATTAA 61.272 55.000 0.00 0.00 45.78 1.40
44 45 0.815615 CAGCTCCCCTGCGGATTAAC 60.816 60.000 0.00 0.00 41.00 2.01
45 46 1.526225 GCTCCCCTGCGGATTAACC 60.526 63.158 0.00 0.00 41.00 2.85
46 47 1.912220 CTCCCCTGCGGATTAACCA 59.088 57.895 0.00 0.00 41.00 3.67
47 48 0.474184 CTCCCCTGCGGATTAACCAT 59.526 55.000 0.00 0.00 41.00 3.55
48 49 0.182537 TCCCCTGCGGATTAACCATG 59.817 55.000 0.00 0.00 34.86 3.66
49 50 0.106719 CCCCTGCGGATTAACCATGT 60.107 55.000 0.00 0.00 38.90 3.21
50 51 1.308998 CCCTGCGGATTAACCATGTC 58.691 55.000 0.00 0.00 38.90 3.06
51 52 1.408127 CCCTGCGGATTAACCATGTCA 60.408 52.381 0.00 0.00 38.90 3.58
52 53 1.670811 CCTGCGGATTAACCATGTCAC 59.329 52.381 0.00 0.00 38.90 3.67
53 54 1.327460 CTGCGGATTAACCATGTCACG 59.673 52.381 0.00 0.00 38.90 4.35
54 55 0.027586 GCGGATTAACCATGTCACGC 59.972 55.000 0.00 0.00 38.90 5.34
55 56 0.655733 CGGATTAACCATGTCACGCC 59.344 55.000 0.00 0.00 38.90 5.68
56 57 1.742411 CGGATTAACCATGTCACGCCT 60.742 52.381 0.00 0.00 38.90 5.52
57 58 1.670811 GGATTAACCATGTCACGCCTG 59.329 52.381 0.00 0.00 38.79 4.85
58 59 1.064060 GATTAACCATGTCACGCCTGC 59.936 52.381 0.00 0.00 0.00 4.85
59 60 0.036164 TTAACCATGTCACGCCTGCT 59.964 50.000 0.00 0.00 0.00 4.24
60 61 0.673333 TAACCATGTCACGCCTGCTG 60.673 55.000 0.00 0.00 0.00 4.41
61 62 3.807538 CCATGTCACGCCTGCTGC 61.808 66.667 0.00 0.00 0.00 5.25
62 63 3.051479 CATGTCACGCCTGCTGCA 61.051 61.111 0.88 0.88 41.33 4.41
63 64 3.052082 ATGTCACGCCTGCTGCAC 61.052 61.111 0.00 0.00 41.33 4.57
66 67 4.560743 TCACGCCTGCTGCACCAA 62.561 61.111 0.00 0.00 41.33 3.67
67 68 4.034258 CACGCCTGCTGCACCAAG 62.034 66.667 0.00 0.00 41.33 3.61
70 71 4.052229 GCCTGCTGCACCAAGCTG 62.052 66.667 0.00 0.00 45.94 4.24
71 72 2.596631 CCTGCTGCACCAAGCTGT 60.597 61.111 0.00 0.00 45.94 4.40
72 73 2.623915 CCTGCTGCACCAAGCTGTC 61.624 63.158 0.00 0.00 45.94 3.51
73 74 2.595463 TGCTGCACCAAGCTGTCC 60.595 61.111 0.00 0.00 45.94 4.02
74 75 3.368571 GCTGCACCAAGCTGTCCC 61.369 66.667 0.00 0.00 45.94 4.46
75 76 2.433446 CTGCACCAAGCTGTCCCT 59.567 61.111 0.00 0.00 45.94 4.20
76 77 1.679311 CTGCACCAAGCTGTCCCTA 59.321 57.895 0.00 0.00 45.94 3.53
77 78 0.036732 CTGCACCAAGCTGTCCCTAA 59.963 55.000 0.00 0.00 45.94 2.69
78 79 0.250727 TGCACCAAGCTGTCCCTAAC 60.251 55.000 0.00 0.00 45.94 2.34
79 80 1.298859 GCACCAAGCTGTCCCTAACG 61.299 60.000 0.00 0.00 41.15 3.18
80 81 0.320374 CACCAAGCTGTCCCTAACGA 59.680 55.000 0.00 0.00 0.00 3.85
81 82 1.053424 ACCAAGCTGTCCCTAACGAA 58.947 50.000 0.00 0.00 0.00 3.85
82 83 1.002087 ACCAAGCTGTCCCTAACGAAG 59.998 52.381 0.00 0.00 0.00 3.79
83 84 1.079503 CAAGCTGTCCCTAACGAAGC 58.920 55.000 0.00 0.00 0.00 3.86
84 85 0.977395 AAGCTGTCCCTAACGAAGCT 59.023 50.000 0.00 0.00 0.00 3.74
85 86 0.977395 AGCTGTCCCTAACGAAGCTT 59.023 50.000 0.00 0.00 0.00 3.74
86 87 1.348036 AGCTGTCCCTAACGAAGCTTT 59.652 47.619 0.00 0.00 0.00 3.51
87 88 2.152016 GCTGTCCCTAACGAAGCTTTT 58.848 47.619 0.00 0.00 0.00 2.27
88 89 3.007614 AGCTGTCCCTAACGAAGCTTTTA 59.992 43.478 0.00 0.00 0.00 1.52
89 90 3.371285 GCTGTCCCTAACGAAGCTTTTAG 59.629 47.826 0.00 5.67 0.00 1.85
90 91 4.566987 CTGTCCCTAACGAAGCTTTTAGT 58.433 43.478 14.10 7.12 0.00 2.24
91 92 4.312443 TGTCCCTAACGAAGCTTTTAGTG 58.688 43.478 14.10 5.85 0.00 2.74
92 93 3.683340 GTCCCTAACGAAGCTTTTAGTGG 59.317 47.826 14.10 13.92 0.00 4.00
93 94 3.007635 CCCTAACGAAGCTTTTAGTGGG 58.992 50.000 14.10 12.83 0.00 4.61
94 95 2.418976 CCTAACGAAGCTTTTAGTGGGC 59.581 50.000 14.10 0.00 0.00 5.36
95 96 2.271944 AACGAAGCTTTTAGTGGGCT 57.728 45.000 0.00 0.00 37.99 5.19
96 97 3.412237 AACGAAGCTTTTAGTGGGCTA 57.588 42.857 0.00 0.00 35.06 3.93
97 98 3.629142 ACGAAGCTTTTAGTGGGCTAT 57.371 42.857 0.00 0.00 35.06 2.97
98 99 3.532542 ACGAAGCTTTTAGTGGGCTATC 58.467 45.455 0.00 0.00 35.06 2.08
99 100 2.540101 CGAAGCTTTTAGTGGGCTATCG 59.460 50.000 0.00 0.00 35.06 2.92
100 101 1.954927 AGCTTTTAGTGGGCTATCGC 58.045 50.000 0.00 0.00 34.31 4.58
101 102 0.582005 GCTTTTAGTGGGCTATCGCG 59.418 55.000 0.00 0.00 36.88 5.87
102 103 1.805120 GCTTTTAGTGGGCTATCGCGA 60.805 52.381 13.09 13.09 36.88 5.87
103 104 2.546778 CTTTTAGTGGGCTATCGCGAA 58.453 47.619 15.24 1.32 36.88 4.70
104 105 1.930567 TTTAGTGGGCTATCGCGAAC 58.069 50.000 15.24 5.40 36.88 3.95
105 106 1.108776 TTAGTGGGCTATCGCGAACT 58.891 50.000 15.24 13.81 36.70 3.01
106 107 1.108776 TAGTGGGCTATCGCGAACTT 58.891 50.000 15.24 0.00 35.14 2.66
107 108 0.179108 AGTGGGCTATCGCGAACTTC 60.179 55.000 15.24 3.41 36.88 3.01
108 109 1.143183 TGGGCTATCGCGAACTTCC 59.857 57.895 15.24 13.68 36.88 3.46
109 110 1.327690 TGGGCTATCGCGAACTTCCT 61.328 55.000 15.24 0.00 36.88 3.36
110 111 0.179081 GGGCTATCGCGAACTTCCTT 60.179 55.000 15.24 0.00 36.88 3.36
111 112 1.068127 GGGCTATCGCGAACTTCCTTA 59.932 52.381 15.24 0.00 36.88 2.69
112 113 2.125685 GGCTATCGCGAACTTCCTTAC 58.874 52.381 15.24 0.00 36.88 2.34
113 114 1.779724 GCTATCGCGAACTTCCTTACG 59.220 52.381 15.24 0.00 0.00 3.18
114 115 2.382519 CTATCGCGAACTTCCTTACGG 58.617 52.381 15.24 0.00 0.00 4.02
115 116 0.529378 ATCGCGAACTTCCTTACGGT 59.471 50.000 15.24 0.00 0.00 4.83
116 117 0.109597 TCGCGAACTTCCTTACGGTC 60.110 55.000 6.20 0.00 0.00 4.79
117 118 0.109412 CGCGAACTTCCTTACGGTCT 60.109 55.000 0.00 0.00 0.00 3.85
118 119 1.668047 CGCGAACTTCCTTACGGTCTT 60.668 52.381 0.00 0.00 0.00 3.01
119 120 1.991264 GCGAACTTCCTTACGGTCTTC 59.009 52.381 0.00 0.00 0.00 2.87
120 121 2.608752 GCGAACTTCCTTACGGTCTTCA 60.609 50.000 0.00 0.00 0.00 3.02
121 122 3.846360 CGAACTTCCTTACGGTCTTCAT 58.154 45.455 0.00 0.00 0.00 2.57
122 123 3.612860 CGAACTTCCTTACGGTCTTCATG 59.387 47.826 0.00 0.00 0.00 3.07
123 124 3.611766 ACTTCCTTACGGTCTTCATGG 57.388 47.619 0.00 0.00 0.00 3.66
124 125 2.280628 CTTCCTTACGGTCTTCATGGC 58.719 52.381 0.00 0.00 0.00 4.40
125 126 0.539986 TCCTTACGGTCTTCATGGCC 59.460 55.000 0.00 0.00 37.00 5.36
126 127 0.463833 CCTTACGGTCTTCATGGCCC 60.464 60.000 0.00 0.00 37.05 5.80
127 128 0.810031 CTTACGGTCTTCATGGCCCG 60.810 60.000 0.00 10.36 45.72 6.13
128 129 2.862674 TTACGGTCTTCATGGCCCGC 62.863 60.000 0.00 0.00 44.14 6.13
129 130 4.473520 CGGTCTTCATGGCCCGCT 62.474 66.667 0.00 0.00 37.05 5.52
130 131 2.044946 GGTCTTCATGGCCCGCTT 60.045 61.111 0.00 0.00 33.37 4.68
131 132 2.409870 GGTCTTCATGGCCCGCTTG 61.410 63.158 0.00 0.00 33.37 4.01
132 133 2.045045 TCTTCATGGCCCGCTTGG 60.045 61.111 0.00 0.00 37.09 3.61
141 142 2.034066 CCCGCTTGGCTTTCCTCA 59.966 61.111 0.00 0.00 0.00 3.86
142 143 2.042831 CCCGCTTGGCTTTCCTCAG 61.043 63.158 0.00 0.00 0.00 3.35
143 144 2.042831 CCGCTTGGCTTTCCTCAGG 61.043 63.158 0.00 0.00 0.00 3.86
144 145 1.003355 CGCTTGGCTTTCCTCAGGA 60.003 57.895 0.00 0.00 0.00 3.86
145 146 0.606401 CGCTTGGCTTTCCTCAGGAA 60.606 55.000 0.34 0.34 40.27 3.36
146 147 1.172175 GCTTGGCTTTCCTCAGGAAG 58.828 55.000 6.17 2.47 43.06 3.46
147 148 1.831580 CTTGGCTTTCCTCAGGAAGG 58.168 55.000 11.34 11.34 43.06 3.46
148 149 1.074566 CTTGGCTTTCCTCAGGAAGGT 59.925 52.381 16.61 0.00 46.32 3.50
149 150 1.149101 TGGCTTTCCTCAGGAAGGTT 58.851 50.000 16.61 0.00 46.32 3.50
150 151 1.499007 TGGCTTTCCTCAGGAAGGTTT 59.501 47.619 16.61 0.00 46.32 3.27
151 152 2.091333 TGGCTTTCCTCAGGAAGGTTTT 60.091 45.455 16.61 0.00 46.32 2.43
152 153 2.965831 GGCTTTCCTCAGGAAGGTTTTT 59.034 45.455 16.61 0.00 46.32 1.94
204 2384 2.611751 TGTGACAAAAGGACACGTCATG 59.388 45.455 0.00 0.00 43.72 3.07
206 2386 0.951558 ACAAAAGGACACGTCATGCC 59.048 50.000 0.00 0.00 0.00 4.40
233 2414 0.958822 AAAAGGACACCGTGCCATTC 59.041 50.000 12.62 0.00 0.00 2.67
361 2542 1.272490 ACATGTCATCGTCTCACGGTT 59.728 47.619 0.00 0.00 42.81 4.44
539 2720 1.405463 TCCATCGACGAGTTGGATCTG 59.595 52.381 14.72 0.46 42.23 2.90
550 2731 2.040412 AGTTGGATCTGAGGTGTTTCCC 59.960 50.000 0.00 0.00 36.75 3.97
584 2765 1.687494 GATCGAGCAAGCACCACGAC 61.687 60.000 0.00 0.00 35.91 4.34
616 2797 1.608717 CCTCCACTCTTCCACCTCCG 61.609 65.000 0.00 0.00 0.00 4.63
617 2798 2.232298 CTCCACTCTTCCACCTCCGC 62.232 65.000 0.00 0.00 0.00 5.54
618 2799 2.266055 CACTCTTCCACCTCCGCC 59.734 66.667 0.00 0.00 0.00 6.13
619 2800 2.120718 ACTCTTCCACCTCCGCCT 59.879 61.111 0.00 0.00 0.00 5.52
620 2801 1.985116 ACTCTTCCACCTCCGCCTC 60.985 63.158 0.00 0.00 0.00 4.70
621 2802 2.683933 TCTTCCACCTCCGCCTCC 60.684 66.667 0.00 0.00 0.00 4.30
639 2820 2.843545 ACCGGCCATTGGTGAGTT 59.156 55.556 0.00 0.00 38.60 3.01
672 2865 3.766691 GAGTTCCGCCGGCCTGTA 61.767 66.667 23.46 2.93 0.00 2.74
693 2886 0.598680 CCTCGCTCGCTTATTCCTGG 60.599 60.000 0.00 0.00 0.00 4.45
759 2982 0.822532 TCGATACTTCTCCGGCCTCC 60.823 60.000 0.00 0.00 0.00 4.30
872 3138 6.216569 CACTAGTTCAGACTTCACTGCTTTA 58.783 40.000 0.00 0.00 37.33 1.85
915 3231 7.662604 TTCTTTTCGTAAATCAAGTCCTACC 57.337 36.000 0.00 0.00 0.00 3.18
929 3245 6.098409 TCAAGTCCTACCTTTCTGTATCATCC 59.902 42.308 0.00 0.00 0.00 3.51
942 3263 9.993454 TTTCTGTATCATCCAGATTTGATCTAG 57.007 33.333 0.00 0.00 38.66 2.43
960 3281 8.475331 TGATCTAGAACGATTTTGAAGTAACC 57.525 34.615 0.00 0.00 0.00 2.85
1094 3416 1.905215 AGGAGATGGTTCTGGTGTCAG 59.095 52.381 0.00 0.00 42.21 3.51
1122 3444 3.430473 TCCTGCATGGAAACGGTTT 57.570 47.368 5.68 5.68 42.94 3.27
1214 3536 9.211410 TCTCTTCTCCATAAATCTCTCTCAATT 57.789 33.333 0.00 0.00 0.00 2.32
1224 3553 6.712241 AATCTCTCTCAATTACAACACACG 57.288 37.500 0.00 0.00 0.00 4.49
1225 3554 3.987868 TCTCTCTCAATTACAACACACGC 59.012 43.478 0.00 0.00 0.00 5.34
1261 3590 0.595053 ATATCTGCTCACGCGTTCCG 60.595 55.000 10.22 0.00 44.21 4.30
1339 3668 1.266718 TGCTGAGCATTTGTTCGTTCC 59.733 47.619 1.40 0.00 31.71 3.62
1383 3712 4.446719 GTCAGTCACCGTCGAAACTAATTT 59.553 41.667 0.00 0.00 0.00 1.82
1443 3772 2.684943 TGGGTGATTCTAATCGGCCTA 58.315 47.619 0.00 0.00 38.26 3.93
1470 3799 3.187022 TCGCGCTAATTATACAGTCGCTA 59.813 43.478 5.56 0.00 36.13 4.26
1511 3840 4.404715 GGTGACAGGTAAGTAAGAGGCATA 59.595 45.833 0.00 0.00 0.00 3.14
1512 3841 5.070580 GGTGACAGGTAAGTAAGAGGCATAT 59.929 44.000 0.00 0.00 0.00 1.78
1513 3842 6.267014 GGTGACAGGTAAGTAAGAGGCATATA 59.733 42.308 0.00 0.00 0.00 0.86
1514 3843 7.038941 GGTGACAGGTAAGTAAGAGGCATATAT 60.039 40.741 0.00 0.00 0.00 0.86
1515 3844 9.021807 GTGACAGGTAAGTAAGAGGCATATATA 57.978 37.037 0.00 0.00 0.00 0.86
1580 3909 7.021196 CACCAAACTAATTAGATTTGTGTCGG 58.979 38.462 21.80 14.37 31.53 4.79
1765 4099 6.424557 CAGAAACAAATCTGCGTTTAACTG 57.575 37.500 0.00 0.00 40.31 3.16
1846 4195 2.500098 CAATATCCCGGTATGGATCGGT 59.500 50.000 0.00 0.00 44.12 4.69
1897 4246 4.124851 TCTTCTCGGCCTTCAAAGATAC 57.875 45.455 0.00 0.00 0.00 2.24
1930 4279 4.122776 GCTACACATACTGTCATCCCTTG 58.877 47.826 0.00 0.00 33.91 3.61
1932 4281 4.478206 ACACATACTGTCATCCCTTGAG 57.522 45.455 0.00 0.00 34.17 3.02
1950 4299 8.431222 TCCCTTGAGTGAAATGAAATGATTTTT 58.569 29.630 0.00 0.00 0.00 1.94
1951 4300 8.715088 CCCTTGAGTGAAATGAAATGATTTTTC 58.285 33.333 0.00 0.00 0.00 2.29
1952 4301 9.485206 CCTTGAGTGAAATGAAATGATTTTTCT 57.515 29.630 0.00 0.00 0.00 2.52
1972 4331 5.688814 TCTAGAATGAGCCCCATGATATG 57.311 43.478 0.00 0.00 35.24 1.78
1974 4333 4.298103 AGAATGAGCCCCATGATATGTC 57.702 45.455 0.00 0.00 35.24 3.06
1976 4335 4.353191 AGAATGAGCCCCATGATATGTCTT 59.647 41.667 0.00 0.00 35.24 3.01
1977 4336 3.777106 TGAGCCCCATGATATGTCTTC 57.223 47.619 0.00 0.00 0.00 2.87
1985 4350 5.188434 CCCATGATATGTCTTCTGTGTGTT 58.812 41.667 0.00 0.00 0.00 3.32
1988 4353 7.044181 CCATGATATGTCTTCTGTGTGTTACT 58.956 38.462 0.00 0.00 0.00 2.24
2008 4373 0.896226 AGGTACGGAAGCTGGAGTTC 59.104 55.000 0.00 0.00 33.68 3.01
2071 4436 2.621338 GTGGAGATGAGCATCGTGAAA 58.379 47.619 4.93 0.00 42.48 2.69
2180 4545 2.608090 GCTCTTGTAATGCCGTAAGTCC 59.392 50.000 0.00 0.00 0.00 3.85
2313 4679 2.527624 TCTGCCCTGGTGCTGTCT 60.528 61.111 8.32 0.00 0.00 3.41
2352 4718 2.230508 AGTAAGAGGAATGAACGACGCA 59.769 45.455 0.00 0.00 0.00 5.24
2370 4736 2.165998 GCATGCAGGTTCTTCCTCTTT 58.834 47.619 14.21 0.00 46.24 2.52
2412 4778 2.417719 GTGGCTCTTCTCGTCAACATT 58.582 47.619 0.00 0.00 0.00 2.71
2448 4814 0.389948 CTGGGACTGTCTGTAACGCC 60.390 60.000 7.85 0.00 0.00 5.68
2551 4917 1.206132 TGTGTTGACCACTGACTTCGT 59.794 47.619 0.00 0.00 44.81 3.85
2555 4921 3.754323 TGTTGACCACTGACTTCGTTTTT 59.246 39.130 0.00 0.00 0.00 1.94
2865 5231 2.159014 TCATTGCATCGGTAGGTACACC 60.159 50.000 0.00 0.00 35.04 4.16
2889 5255 0.392706 TCACCACAGCACAGAATCGT 59.607 50.000 0.00 0.00 0.00 3.73
2933 5299 4.945543 TGATGCATGACATATATTGGCCTC 59.054 41.667 2.46 0.00 39.84 4.70
2967 5333 4.634883 CCATGCAAGCAGATGATACTATCC 59.365 45.833 0.00 0.00 0.00 2.59
2994 5360 0.395311 TACCGTTCGCTCTCATCCCT 60.395 55.000 0.00 0.00 0.00 4.20
3045 5411 2.564721 GGGCCAGTGCAACAACTCC 61.565 63.158 4.39 0.00 41.43 3.85
3047 5413 1.360192 GCCAGTGCAACAACTCCAC 59.640 57.895 0.00 0.00 41.43 4.02
3057 5423 3.127030 GCAACAACTCCACCTATGTAAGC 59.873 47.826 0.00 0.00 0.00 3.09
3062 5428 2.840651 ACTCCACCTATGTAAGCAAGCT 59.159 45.455 0.00 0.00 0.00 3.74
3063 5429 3.264450 ACTCCACCTATGTAAGCAAGCTT 59.736 43.478 12.42 12.42 39.83 3.74
3074 5440 3.396260 AAGCAAGCTTACGAACTACCA 57.604 42.857 5.34 0.00 34.05 3.25
3078 5444 3.682858 GCAAGCTTACGAACTACCAATCA 59.317 43.478 0.00 0.00 0.00 2.57
3082 5448 7.254795 GCAAGCTTACGAACTACCAATCAATAT 60.255 37.037 0.00 0.00 0.00 1.28
3127 5497 4.680440 GCTGTGGAAGTGTGGAATTTGTTT 60.680 41.667 0.00 0.00 0.00 2.83
3191 5561 4.407365 TCTCATGGACGCTAGGATTCATA 58.593 43.478 0.00 0.00 0.00 2.15
3233 5603 5.344743 ACTTCCTCAGCTCGAAATTGATA 57.655 39.130 0.00 0.00 0.00 2.15
3266 5636 1.141881 CAACTCGCTGCCGACCTAT 59.858 57.895 0.00 0.00 38.82 2.57
3398 5768 0.105778 TGCAGGACATTGACGACACA 59.894 50.000 0.00 0.00 0.00 3.72
3556 5928 6.224420 AGTTTTTGTAGATCGTGTTAGTGC 57.776 37.500 0.00 0.00 0.00 4.40
3567 5939 0.320421 TGTTAGTGCGGTCTTCTGCC 60.320 55.000 0.00 0.00 44.62 4.85
3583 5955 6.264067 GTCTTCTGCCAATGATAAATAGGCTT 59.736 38.462 0.00 0.00 45.42 4.35
3593 5965 6.588719 TGATAAATAGGCTTTGCAAGTGTT 57.411 33.333 0.00 0.00 0.00 3.32
3674 6047 3.354131 TTTTTGACCGCAAACTGCC 57.646 47.368 0.00 0.00 43.27 4.85
3685 6058 3.909086 AAACTGCCGGAGCTCTGCC 62.909 63.158 17.68 6.83 40.80 4.85
3705 6078 4.093743 GCCTTTTCAATTAAGAAGGGGGA 58.906 43.478 0.27 0.00 39.21 4.81
3706 6079 4.160439 GCCTTTTCAATTAAGAAGGGGGAG 59.840 45.833 0.27 0.00 39.21 4.30
3710 6083 6.911250 TTTCAATTAAGAAGGGGGAGAAAC 57.089 37.500 0.00 0.00 0.00 2.78
3723 6096 1.228552 AGAAACCGCACAATGGGCT 60.229 52.632 5.74 0.00 0.00 5.19
3731 6104 1.203052 CGCACAATGGGCTGAGAAATT 59.797 47.619 5.74 0.00 0.00 1.82
3749 6122 7.502226 TGAGAAATTCAGCTTACAGAGGAAAAA 59.498 33.333 0.00 0.00 0.00 1.94
3791 6164 2.237392 AGGAGGGAGACACAAACTATGC 59.763 50.000 0.00 0.00 0.00 3.14
3796 6169 3.375299 GGGAGACACAAACTATGCACATC 59.625 47.826 0.00 0.00 0.00 3.06
3798 6171 4.331168 GGAGACACAAACTATGCACATCTC 59.669 45.833 0.00 0.00 0.00 2.75
3799 6172 4.256920 AGACACAAACTATGCACATCTCC 58.743 43.478 0.00 0.00 0.00 3.71
3800 6173 4.002982 GACACAAACTATGCACATCTCCA 58.997 43.478 0.00 0.00 0.00 3.86
3801 6174 4.005650 ACACAAACTATGCACATCTCCAG 58.994 43.478 0.00 0.00 0.00 3.86
3802 6175 4.256110 CACAAACTATGCACATCTCCAGA 58.744 43.478 0.00 0.00 0.00 3.86
3803 6176 4.331992 CACAAACTATGCACATCTCCAGAG 59.668 45.833 0.00 0.00 0.00 3.35
3804 6177 2.906691 ACTATGCACATCTCCAGAGC 57.093 50.000 0.00 0.00 0.00 4.09
3805 6178 1.415659 ACTATGCACATCTCCAGAGCC 59.584 52.381 0.00 0.00 0.00 4.70
3806 6179 1.693062 CTATGCACATCTCCAGAGCCT 59.307 52.381 0.00 0.00 0.00 4.58
3807 6180 0.180642 ATGCACATCTCCAGAGCCTG 59.819 55.000 0.00 0.00 0.00 4.85
3808 6181 1.196766 TGCACATCTCCAGAGCCTGT 61.197 55.000 2.18 0.00 0.00 4.00
3809 6182 0.461693 GCACATCTCCAGAGCCTGTC 60.462 60.000 2.18 0.00 0.00 3.51
3810 6183 0.900421 CACATCTCCAGAGCCTGTCA 59.100 55.000 2.18 0.00 0.00 3.58
3811 6184 1.277273 CACATCTCCAGAGCCTGTCAA 59.723 52.381 2.18 0.00 0.00 3.18
3812 6185 1.554160 ACATCTCCAGAGCCTGTCAAG 59.446 52.381 2.18 0.00 0.00 3.02
3813 6186 1.829849 CATCTCCAGAGCCTGTCAAGA 59.170 52.381 2.18 2.92 0.00 3.02
3814 6187 1.261480 TCTCCAGAGCCTGTCAAGAC 58.739 55.000 0.00 0.00 0.00 3.01
3822 6195 3.006323 AGAGCCTGTCAAGACACTAACAG 59.994 47.826 0.00 0.00 39.04 3.16
3828 6201 6.281405 CCTGTCAAGACACTAACAGTTACTT 58.719 40.000 0.00 0.00 37.92 2.24
3829 6202 7.431249 CCTGTCAAGACACTAACAGTTACTTA 58.569 38.462 0.00 0.00 37.92 2.24
3831 6204 8.004087 TGTCAAGACACTAACAGTTACTTACT 57.996 34.615 0.00 0.00 36.21 2.24
3832 6205 8.133627 TGTCAAGACACTAACAGTTACTTACTC 58.866 37.037 0.00 0.00 36.21 2.59
3833 6206 8.351461 GTCAAGACACTAACAGTTACTTACTCT 58.649 37.037 0.00 0.00 33.85 3.24
3834 6207 8.566260 TCAAGACACTAACAGTTACTTACTCTC 58.434 37.037 0.00 0.00 33.85 3.20
3835 6208 7.131498 AGACACTAACAGTTACTTACTCTCG 57.869 40.000 0.00 0.00 33.85 4.04
3862 6235 3.605946 CCTCTAGAGGGTCACAGCT 57.394 57.895 28.68 0.00 44.87 4.24
3863 6236 1.398692 CCTCTAGAGGGTCACAGCTC 58.601 60.000 28.68 0.00 44.87 4.09
3864 6237 1.064017 CCTCTAGAGGGTCACAGCTCT 60.064 57.143 28.68 0.00 44.87 4.09
3865 6238 2.622977 CCTCTAGAGGGTCACAGCTCTT 60.623 54.545 28.68 0.00 44.87 2.85
3866 6239 2.426738 CTCTAGAGGGTCACAGCTCTTG 59.573 54.545 12.27 0.00 0.00 3.02
3867 6240 2.175202 CTAGAGGGTCACAGCTCTTGT 58.825 52.381 0.00 0.00 41.94 3.16
3868 6241 0.972883 AGAGGGTCACAGCTCTTGTC 59.027 55.000 0.00 0.00 38.16 3.18
3869 6242 0.972883 GAGGGTCACAGCTCTTGTCT 59.027 55.000 0.00 0.00 38.16 3.41
3870 6243 1.346068 GAGGGTCACAGCTCTTGTCTT 59.654 52.381 0.00 0.00 38.16 3.01
3873 6246 2.485479 GGGTCACAGCTCTTGTCTTCAA 60.485 50.000 0.00 0.00 38.16 2.69
3874 6247 3.206150 GGTCACAGCTCTTGTCTTCAAA 58.794 45.455 0.00 0.00 38.16 2.69
3875 6248 3.249559 GGTCACAGCTCTTGTCTTCAAAG 59.750 47.826 0.00 0.00 38.16 2.77
3876 6249 3.873952 GTCACAGCTCTTGTCTTCAAAGT 59.126 43.478 0.00 0.00 38.16 2.66
3877 6250 4.333926 GTCACAGCTCTTGTCTTCAAAGTT 59.666 41.667 0.00 0.00 38.16 2.66
3878 6251 4.572389 TCACAGCTCTTGTCTTCAAAGTTC 59.428 41.667 0.00 0.00 38.16 3.01
3879 6252 4.574013 CACAGCTCTTGTCTTCAAAGTTCT 59.426 41.667 0.00 0.00 38.16 3.01
3880 6253 5.065731 CACAGCTCTTGTCTTCAAAGTTCTT 59.934 40.000 0.00 0.00 38.16 2.52
3881 6254 5.649831 ACAGCTCTTGTCTTCAAAGTTCTTT 59.350 36.000 0.00 0.00 33.87 2.52
3882 6255 5.970023 CAGCTCTTGTCTTCAAAGTTCTTTG 59.030 40.000 16.33 16.33 32.87 2.77
3883 6256 5.067023 AGCTCTTGTCTTCAAAGTTCTTTGG 59.933 40.000 20.41 9.34 32.87 3.28
3884 6257 5.163612 GCTCTTGTCTTCAAAGTTCTTTGGT 60.164 40.000 20.41 0.00 32.87 3.67
3885 6258 6.625960 GCTCTTGTCTTCAAAGTTCTTTGGTT 60.626 38.462 20.41 0.00 32.87 3.67
3891 6267 7.812669 TGTCTTCAAAGTTCTTTGGTTTCTTTC 59.187 33.333 20.41 8.04 32.99 2.62
3894 6270 6.998802 TCAAAGTTCTTTGGTTTCTTTCCAA 58.001 32.000 20.41 0.00 42.29 3.53
3896 6272 4.993905 AGTTCTTTGGTTTCTTTCCAACG 58.006 39.130 0.00 0.00 43.45 4.10
3913 6289 0.387112 ACGAAACGTGCCATGCAATG 60.387 50.000 0.00 0.00 41.47 2.82
3944 6320 0.804989 CGAGCCCAAATCTTTTCGCT 59.195 50.000 0.00 0.00 0.00 4.93
3947 6323 0.173481 GCCCAAATCTTTTCGCTCCC 59.827 55.000 0.00 0.00 0.00 4.30
3955 6346 1.614903 TCTTTTCGCTCCCTCGTTGTA 59.385 47.619 0.00 0.00 0.00 2.41
3957 6348 1.250328 TTTCGCTCCCTCGTTGTAGA 58.750 50.000 0.00 0.00 0.00 2.59
3959 6350 0.035725 TCGCTCCCTCGTTGTAGAGA 60.036 55.000 0.00 0.00 40.57 3.10
3974 6365 3.442625 TGTAGAGATTGTTCCGACGATGT 59.557 43.478 0.00 0.00 29.77 3.06
3976 6367 3.926616 AGAGATTGTTCCGACGATGTTT 58.073 40.909 0.00 0.00 29.77 2.83
3977 6368 3.679980 AGAGATTGTTCCGACGATGTTTG 59.320 43.478 0.00 0.00 29.77 2.93
3981 6372 1.232119 GTTCCGACGATGTTTGGGTT 58.768 50.000 0.00 0.00 0.00 4.11
3982 6373 1.196127 GTTCCGACGATGTTTGGGTTC 59.804 52.381 0.00 0.00 0.00 3.62
3983 6374 0.682852 TCCGACGATGTTTGGGTTCT 59.317 50.000 0.00 0.00 0.00 3.01
3984 6375 1.076332 CCGACGATGTTTGGGTTCTC 58.924 55.000 0.00 0.00 0.00 2.87
3993 6953 5.626809 CGATGTTTGGGTTCTCATAAGAGGA 60.627 44.000 0.00 0.00 42.34 3.71
4027 6987 4.288105 CCCCATACATGCTTAGAGAAGGAT 59.712 45.833 0.00 0.00 43.92 3.24
4034 6994 3.034635 TGCTTAGAGAAGGATCAGTCCC 58.965 50.000 0.00 0.00 46.34 4.46
4089 7049 6.212589 TGGTCACATAAACAACAGAGAGGATA 59.787 38.462 0.00 0.00 0.00 2.59
4090 7050 7.092891 TGGTCACATAAACAACAGAGAGGATAT 60.093 37.037 0.00 0.00 0.00 1.63
4094 7054 9.166173 CACATAAACAACAGAGAGGATATTTCA 57.834 33.333 0.00 0.00 0.00 2.69
4117 7077 2.224769 CCAGCCTCTCTTTTGTAACCCA 60.225 50.000 0.00 0.00 0.00 4.51
4186 7163 1.283905 GGTTTACCTGTGGCATAGGGT 59.716 52.381 30.47 20.80 39.71 4.34
4244 7221 0.179045 GAATATGTGGCCCGAGCAGT 60.179 55.000 0.00 0.00 42.56 4.40
4380 7374 3.796844 GCAAAGCCTTCCTTGACAGAAAC 60.797 47.826 0.00 0.00 33.01 2.78
4391 7385 4.036852 CCTTGACAGAAACCAGTCTTTTCC 59.963 45.833 0.00 0.00 34.07 3.13
4399 7393 2.047830 ACCAGTCTTTTCCTCGAGGTT 58.952 47.619 30.17 6.55 36.34 3.50
4410 7404 0.040067 CTCGAGGTTTTGGCAAGCAC 60.040 55.000 3.91 1.40 0.00 4.40
4429 7423 1.823041 GGGAGCAATCTCAGCAGGC 60.823 63.158 0.00 0.00 41.13 4.85
4446 7440 1.221523 AGGCTCCTGACCATCTATCCA 59.778 52.381 0.00 0.00 0.00 3.41
4447 7441 2.158035 AGGCTCCTGACCATCTATCCAT 60.158 50.000 0.00 0.00 0.00 3.41
4448 7442 2.235898 GGCTCCTGACCATCTATCCATC 59.764 54.545 0.00 0.00 0.00 3.51
4449 7443 3.172339 GCTCCTGACCATCTATCCATCT 58.828 50.000 0.00 0.00 0.00 2.90
4450 7444 3.582208 GCTCCTGACCATCTATCCATCTT 59.418 47.826 0.00 0.00 0.00 2.40
4451 7445 4.041444 GCTCCTGACCATCTATCCATCTTT 59.959 45.833 0.00 0.00 0.00 2.52
4452 7446 5.792741 CTCCTGACCATCTATCCATCTTTC 58.207 45.833 0.00 0.00 0.00 2.62
4453 7447 4.594920 TCCTGACCATCTATCCATCTTTCC 59.405 45.833 0.00 0.00 0.00 3.13
4454 7448 4.263243 CCTGACCATCTATCCATCTTTCCC 60.263 50.000 0.00 0.00 0.00 3.97
4455 7449 4.570926 TGACCATCTATCCATCTTTCCCT 58.429 43.478 0.00 0.00 0.00 4.20
4456 7450 5.726560 TGACCATCTATCCATCTTTCCCTA 58.273 41.667 0.00 0.00 0.00 3.53
4457 7451 5.782331 TGACCATCTATCCATCTTTCCCTAG 59.218 44.000 0.00 0.00 0.00 3.02
4458 7452 5.982391 ACCATCTATCCATCTTTCCCTAGA 58.018 41.667 0.00 0.00 0.00 2.43
4459 7453 6.393897 ACCATCTATCCATCTTTCCCTAGAA 58.606 40.000 0.00 0.00 0.00 2.10
4460 7454 6.851836 ACCATCTATCCATCTTTCCCTAGAAA 59.148 38.462 0.00 0.00 39.70 2.52
4461 7455 7.164803 CCATCTATCCATCTTTCCCTAGAAAC 58.835 42.308 0.00 0.00 37.07 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.236006 GGGAGCTGTATATCACAATCATTAATT 57.764 33.333 0.00 0.00 36.48 1.40
7 8 7.831193 GGGGAGCTGTATATCACAATCATTAAT 59.169 37.037 0.00 0.00 36.48 1.40
8 9 7.017551 AGGGGAGCTGTATATCACAATCATTAA 59.982 37.037 0.00 0.00 36.48 1.40
9 10 6.501805 AGGGGAGCTGTATATCACAATCATTA 59.498 38.462 0.00 0.00 36.48 1.90
10 11 5.311649 AGGGGAGCTGTATATCACAATCATT 59.688 40.000 0.00 0.00 36.48 2.57
11 12 4.848660 AGGGGAGCTGTATATCACAATCAT 59.151 41.667 0.00 0.00 36.48 2.45
12 13 4.040829 CAGGGGAGCTGTATATCACAATCA 59.959 45.833 0.00 0.00 36.48 2.57
13 14 4.573900 CAGGGGAGCTGTATATCACAATC 58.426 47.826 0.00 0.00 36.48 2.67
14 15 3.244700 GCAGGGGAGCTGTATATCACAAT 60.245 47.826 0.00 0.00 36.48 2.71
15 16 2.104792 GCAGGGGAGCTGTATATCACAA 59.895 50.000 0.00 0.00 36.48 3.33
16 17 1.694150 GCAGGGGAGCTGTATATCACA 59.306 52.381 0.00 0.00 35.30 3.58
17 18 1.337260 CGCAGGGGAGCTGTATATCAC 60.337 57.143 0.00 0.00 0.00 3.06
18 19 0.969149 CGCAGGGGAGCTGTATATCA 59.031 55.000 0.00 0.00 0.00 2.15
19 20 3.822607 CGCAGGGGAGCTGTATATC 57.177 57.895 0.00 0.00 0.00 1.63
33 34 1.327460 CGTGACATGGTTAATCCGCAG 59.673 52.381 0.00 0.00 39.52 5.18
34 35 1.364721 CGTGACATGGTTAATCCGCA 58.635 50.000 0.00 0.00 39.52 5.69
35 36 0.027586 GCGTGACATGGTTAATCCGC 59.972 55.000 0.00 0.00 39.52 5.54
36 37 0.655733 GGCGTGACATGGTTAATCCG 59.344 55.000 0.00 0.00 39.52 4.18
37 38 1.670811 CAGGCGTGACATGGTTAATCC 59.329 52.381 0.00 0.00 0.00 3.01
38 39 1.064060 GCAGGCGTGACATGGTTAATC 59.936 52.381 11.29 0.00 0.00 1.75
39 40 1.094785 GCAGGCGTGACATGGTTAAT 58.905 50.000 11.29 0.00 0.00 1.40
40 41 0.036164 AGCAGGCGTGACATGGTTAA 59.964 50.000 11.29 0.00 0.00 2.01
41 42 0.673333 CAGCAGGCGTGACATGGTTA 60.673 55.000 11.29 0.00 0.00 2.85
42 43 1.968017 CAGCAGGCGTGACATGGTT 60.968 57.895 11.29 0.00 0.00 3.67
43 44 2.359107 CAGCAGGCGTGACATGGT 60.359 61.111 11.29 0.00 0.00 3.55
44 45 3.807538 GCAGCAGGCGTGACATGG 61.808 66.667 11.29 0.00 0.00 3.66
53 54 4.052229 CAGCTTGGTGCAGCAGGC 62.052 66.667 36.93 36.93 45.94 4.85
54 55 2.596631 ACAGCTTGGTGCAGCAGG 60.597 61.111 22.33 22.33 45.94 4.85
55 56 2.623915 GGACAGCTTGGTGCAGCAG 61.624 63.158 19.25 13.87 45.94 4.24
56 57 2.595463 GGACAGCTTGGTGCAGCA 60.595 61.111 15.99 15.99 45.94 4.41
57 58 2.469465 TAGGGACAGCTTGGTGCAGC 62.469 60.000 9.47 9.47 45.94 5.25
58 59 0.036732 TTAGGGACAGCTTGGTGCAG 59.963 55.000 0.00 0.00 45.94 4.41
59 60 0.250727 GTTAGGGACAGCTTGGTGCA 60.251 55.000 0.00 0.00 45.94 4.57
60 61 1.298859 CGTTAGGGACAGCTTGGTGC 61.299 60.000 0.00 0.00 43.29 5.01
61 62 0.320374 TCGTTAGGGACAGCTTGGTG 59.680 55.000 0.00 0.00 0.00 4.17
62 63 1.002087 CTTCGTTAGGGACAGCTTGGT 59.998 52.381 0.00 0.00 0.00 3.67
63 64 1.726853 CTTCGTTAGGGACAGCTTGG 58.273 55.000 0.00 0.00 0.00 3.61
64 65 1.079503 GCTTCGTTAGGGACAGCTTG 58.920 55.000 0.00 0.00 0.00 4.01
65 66 0.977395 AGCTTCGTTAGGGACAGCTT 59.023 50.000 0.00 0.00 0.00 3.74
66 67 0.977395 AAGCTTCGTTAGGGACAGCT 59.023 50.000 0.00 0.00 0.00 4.24
67 68 1.809684 AAAGCTTCGTTAGGGACAGC 58.190 50.000 0.00 0.00 0.00 4.40
68 69 4.389077 CACTAAAAGCTTCGTTAGGGACAG 59.611 45.833 17.96 0.45 33.33 3.51
69 70 4.312443 CACTAAAAGCTTCGTTAGGGACA 58.688 43.478 17.96 0.00 33.33 4.02
70 71 3.683340 CCACTAAAAGCTTCGTTAGGGAC 59.317 47.826 17.98 0.00 33.33 4.46
71 72 3.307199 CCCACTAAAAGCTTCGTTAGGGA 60.307 47.826 17.98 0.00 33.33 4.20
72 73 3.007635 CCCACTAAAAGCTTCGTTAGGG 58.992 50.000 17.96 14.98 32.60 3.53
73 74 2.418976 GCCCACTAAAAGCTTCGTTAGG 59.581 50.000 17.96 10.32 32.60 2.69
74 75 3.335579 AGCCCACTAAAAGCTTCGTTAG 58.664 45.455 13.91 13.91 31.27 2.34
75 76 3.412237 AGCCCACTAAAAGCTTCGTTA 57.588 42.857 0.00 0.00 31.27 3.18
76 77 2.271944 AGCCCACTAAAAGCTTCGTT 57.728 45.000 0.00 0.00 31.27 3.85
77 78 3.532542 GATAGCCCACTAAAAGCTTCGT 58.467 45.455 0.00 0.00 38.06 3.85
78 79 2.540101 CGATAGCCCACTAAAAGCTTCG 59.460 50.000 0.00 0.00 38.06 3.79
108 109 0.810031 CGGGCCATGAAGACCGTAAG 60.810 60.000 4.39 0.00 41.34 2.34
109 110 1.219664 CGGGCCATGAAGACCGTAA 59.780 57.895 4.39 0.00 41.34 3.18
110 111 2.897207 CGGGCCATGAAGACCGTA 59.103 61.111 4.39 0.00 41.34 4.02
113 114 2.044946 AAGCGGGCCATGAAGACC 60.045 61.111 4.39 0.00 0.00 3.85
114 115 2.409870 CCAAGCGGGCCATGAAGAC 61.410 63.158 4.39 0.00 0.00 3.01
115 116 2.045045 CCAAGCGGGCCATGAAGA 60.045 61.111 4.39 0.00 0.00 2.87
124 125 2.034066 TGAGGAAAGCCAAGCGGG 59.966 61.111 0.00 0.00 40.85 6.13
125 126 2.042831 CCTGAGGAAAGCCAAGCGG 61.043 63.158 0.00 0.00 36.29 5.52
126 127 0.606401 TTCCTGAGGAAAGCCAAGCG 60.606 55.000 12.35 0.00 38.93 4.68
127 128 1.172175 CTTCCTGAGGAAAGCCAAGC 58.828 55.000 15.79 0.00 41.54 4.01
149 150 6.194967 AGGAAAGTCCCTCAGAAAAGAAAAA 58.805 36.000 0.00 0.00 37.19 1.94
150 151 5.766590 AGGAAAGTCCCTCAGAAAAGAAAA 58.233 37.500 0.00 0.00 37.19 2.29
151 152 5.388599 AGGAAAGTCCCTCAGAAAAGAAA 57.611 39.130 0.00 0.00 37.19 2.52
276 2457 1.076533 GCCGTGATATATGGGCGTCG 61.077 60.000 0.00 0.00 35.59 5.12
284 2465 1.736645 GCCGCGTGCCGTGATATAT 60.737 57.895 4.92 0.00 39.94 0.86
539 2720 2.640316 AGTCTGTTGGGAAACACCTC 57.360 50.000 0.00 0.00 38.98 3.85
550 2731 3.622828 CTCGATCGATGGTAGTCTGTTG 58.377 50.000 19.78 0.00 0.00 3.33
584 2765 4.821589 GGAGGGCGCGAGGTCTTG 62.822 72.222 12.10 0.00 0.00 3.02
606 2787 3.319198 GTGGAGGCGGAGGTGGAA 61.319 66.667 0.00 0.00 0.00 3.53
617 2798 4.047125 ACCAATGGCCGGTGGAGG 62.047 66.667 26.93 12.27 38.36 4.30
639 2820 4.828829 GGAACTCCGATCTAAGGAACAAA 58.171 43.478 0.00 0.00 37.32 2.83
664 2845 4.208686 GAGCGAGGGTACAGGCCG 62.209 72.222 0.00 0.00 0.00 6.13
667 2848 1.381928 TAAGCGAGCGAGGGTACAGG 61.382 60.000 0.00 0.00 0.00 4.00
668 2849 0.669077 ATAAGCGAGCGAGGGTACAG 59.331 55.000 0.00 0.00 0.00 2.74
672 2865 1.043673 AGGAATAAGCGAGCGAGGGT 61.044 55.000 0.00 0.00 0.00 4.34
693 2886 1.790896 GCGTGACGCGTTAAAAGGC 60.791 57.895 16.19 13.15 44.55 4.35
759 2982 1.155042 GAACAGAGAGGCAAGTGCAG 58.845 55.000 5.52 0.00 44.36 4.41
792 3015 2.383527 GCTTGGCGACGAACAGGAG 61.384 63.158 0.00 0.00 0.00 3.69
872 3138 2.080286 AAATCTACGCACGAACAGCT 57.920 45.000 0.00 0.00 0.00 4.24
915 3231 8.905660 AGATCAAATCTGGATGATACAGAAAG 57.094 34.615 12.04 4.86 46.89 2.62
929 3245 9.699985 CTTCAAAATCGTTCTAGATCAAATCTG 57.300 33.333 0.00 0.00 40.51 2.90
959 3280 5.875910 TGCATTGCATTGGATTAAAAGAAGG 59.124 36.000 7.38 0.00 31.71 3.46
960 3281 6.971527 TGCATTGCATTGGATTAAAAGAAG 57.028 33.333 7.38 0.00 31.71 2.85
1122 3444 2.359850 GGTCCAATGTGGCGCAGA 60.360 61.111 10.83 0.00 37.47 4.26
1214 3536 3.930229 GGAATCATACTGCGTGTGTTGTA 59.070 43.478 5.64 0.00 0.00 2.41
1224 3553 6.312426 GCAGATATGTACTGGAATCATACTGC 59.688 42.308 0.00 0.00 39.16 4.40
1225 3554 7.609960 AGCAGATATGTACTGGAATCATACTG 58.390 38.462 0.00 0.00 36.09 2.74
1261 3590 2.940410 TCCGTTTCCACTGTTTCAGTTC 59.060 45.455 0.00 0.00 42.59 3.01
1383 3712 3.181480 CGAAACAGGGAAGGAAGCAAAAA 60.181 43.478 0.00 0.00 0.00 1.94
1443 3772 5.342525 CGACTGTATAATTAGCGCGAAGATT 59.657 40.000 12.10 8.42 0.00 2.40
1470 3799 1.210478 ACCACGCCAAGATTAGCTGAT 59.790 47.619 0.00 0.00 0.00 2.90
1580 3909 4.394729 TCCCTGTTTTAGTTGATGTCCAC 58.605 43.478 0.00 0.00 0.00 4.02
1735 4068 5.885881 ACGCAGATTTGTTTCTGTTGTTTA 58.114 33.333 3.65 0.00 44.10 2.01
1744 4078 5.968848 TCACAGTTAAACGCAGATTTGTTTC 59.031 36.000 0.00 0.00 39.00 2.78
1765 4099 9.357652 ACTGCAAATCACAAATATAAACATCAC 57.642 29.630 0.00 0.00 0.00 3.06
1846 4195 2.679059 GCTAGAGCCAGCAATGAGAACA 60.679 50.000 0.00 0.00 41.40 3.18
1897 4246 0.539986 ATGTGTAGCTGGTTACCCCG 59.460 55.000 0.00 0.00 35.15 5.73
1914 4263 4.743057 TCACTCAAGGGATGACAGTATG 57.257 45.455 0.00 0.00 46.00 2.39
1915 4264 5.762179 TTTCACTCAAGGGATGACAGTAT 57.238 39.130 0.00 0.00 33.47 2.12
1916 4265 5.248248 TCATTTCACTCAAGGGATGACAGTA 59.752 40.000 0.00 0.00 33.47 2.74
1917 4266 4.042062 TCATTTCACTCAAGGGATGACAGT 59.958 41.667 0.00 0.00 33.47 3.55
1918 4267 4.582869 TCATTTCACTCAAGGGATGACAG 58.417 43.478 0.00 0.00 33.47 3.51
1919 4268 4.639078 TCATTTCACTCAAGGGATGACA 57.361 40.909 0.00 0.00 33.47 3.58
1950 4299 5.096521 ACATATCATGGGGCTCATTCTAGA 58.903 41.667 0.00 0.00 32.92 2.43
1951 4300 5.189342 AGACATATCATGGGGCTCATTCTAG 59.811 44.000 0.00 0.00 32.92 2.43
1952 4301 5.096521 AGACATATCATGGGGCTCATTCTA 58.903 41.667 0.00 0.00 32.92 2.10
1954 4303 4.298103 AGACATATCATGGGGCTCATTC 57.702 45.455 0.00 0.00 32.92 2.67
1972 4331 5.388944 CGTACCTAGTAACACACAGAAGAC 58.611 45.833 0.00 0.00 0.00 3.01
1974 4333 4.456911 TCCGTACCTAGTAACACACAGAAG 59.543 45.833 0.00 0.00 0.00 2.85
1976 4335 4.019792 TCCGTACCTAGTAACACACAGA 57.980 45.455 0.00 0.00 0.00 3.41
1977 4336 4.730657 CTTCCGTACCTAGTAACACACAG 58.269 47.826 0.00 0.00 0.00 3.66
1985 4350 2.240667 ACTCCAGCTTCCGTACCTAGTA 59.759 50.000 0.00 0.00 0.00 1.82
1988 4353 2.097825 GAACTCCAGCTTCCGTACCTA 58.902 52.381 0.00 0.00 0.00 3.08
2008 4373 3.289834 ACCAGCAGCGCAACCAAG 61.290 61.111 11.47 0.00 0.00 3.61
2180 4545 6.572119 TGGCAAATGGCAGTTAAATTCTGTAG 60.572 38.462 5.46 0.00 46.12 2.74
2217 4582 4.518590 TGTAAGATGCAGCAGCTAACAAAA 59.481 37.500 14.94 0.00 42.74 2.44
2224 4590 2.014857 CACATGTAAGATGCAGCAGCT 58.985 47.619 7.55 7.55 42.74 4.24
2229 4595 9.229784 GAATTAATGTTCACATGTAAGATGCAG 57.770 33.333 0.00 0.00 36.56 4.41
2412 4778 2.169978 CCCAGAGACAGAGATGATTGCA 59.830 50.000 0.00 0.00 0.00 4.08
2463 4829 2.357517 CACTTGGCGGCGTTCTCT 60.358 61.111 9.37 0.00 0.00 3.10
2555 4921 3.007506 ACCATCGACCATGTACAGTTCAA 59.992 43.478 0.33 0.00 0.00 2.69
2569 4935 6.093495 TCAATCTTTCATAAACCACCATCGAC 59.907 38.462 0.00 0.00 0.00 4.20
2865 5231 1.013596 TCTGTGCTGTGGTGAAAACG 58.986 50.000 0.00 0.00 0.00 3.60
2889 5255 7.933396 CATCATGCAGTATTCAGGATGTTTAA 58.067 34.615 8.82 0.00 43.59 1.52
2933 5299 0.937304 CTTGCATGGACGATAACCCG 59.063 55.000 0.00 0.00 0.00 5.28
2967 5333 3.123674 AGCGAACGGTAGCTCAAAG 57.876 52.632 0.74 0.00 39.98 2.77
2994 5360 2.763933 CTGCTGCTGAACTTGAGAAGA 58.236 47.619 0.00 0.00 0.00 2.87
3045 5411 4.430007 TCGTAAGCTTGCTTACATAGGTG 58.570 43.478 31.68 20.26 39.15 4.00
3047 5413 5.109903 AGTTCGTAAGCTTGCTTACATAGG 58.890 41.667 31.68 21.03 39.15 2.57
3057 5423 5.856126 TTGATTGGTAGTTCGTAAGCTTG 57.144 39.130 9.86 0.00 37.18 4.01
3087 5453 9.868277 CTTCCACAGCCAAAAATATAAACAATA 57.132 29.630 0.00 0.00 0.00 1.90
3127 5497 2.779430 AGGTACATGGATGGATTCAGCA 59.221 45.455 0.00 0.00 0.00 4.41
3191 5561 5.786264 AGTAGACGTTTATCCCGATGATT 57.214 39.130 0.00 0.00 34.76 2.57
3351 5721 1.127582 GCGAGACATGAACTTGACTGC 59.872 52.381 0.00 0.00 0.00 4.40
3398 5768 0.108585 TGGCAACCTTCGCTTTCTCT 59.891 50.000 0.00 0.00 0.00 3.10
3556 5928 5.180117 CCTATTTATCATTGGCAGAAGACCG 59.820 44.000 0.00 0.00 0.00 4.79
3583 5955 0.814457 AAAGCCGTGAACACTTGCAA 59.186 45.000 0.00 0.00 31.76 4.08
3593 5965 0.318869 CAATTGCAGCAAAGCCGTGA 60.319 50.000 12.97 0.00 0.00 4.35
3674 6047 1.457346 ATTGAAAAGGCAGAGCTCCG 58.543 50.000 10.93 0.00 0.00 4.63
3685 6058 7.378966 GTTTCTCCCCCTTCTTAATTGAAAAG 58.621 38.462 0.00 0.00 0.00 2.27
3705 6078 1.228552 AGCCCATTGTGCGGTTTCT 60.229 52.632 0.00 0.00 0.00 2.52
3706 6079 1.080569 CAGCCCATTGTGCGGTTTC 60.081 57.895 0.00 0.00 0.00 2.78
3710 6083 1.243342 TTTCTCAGCCCATTGTGCGG 61.243 55.000 0.00 0.00 0.00 5.69
3723 6096 5.745312 TCCTCTGTAAGCTGAATTTCTCA 57.255 39.130 0.00 0.00 0.00 3.27
3762 6135 2.777692 TGTGTCTCCCTCCTGTCTTTTT 59.222 45.455 0.00 0.00 0.00 1.94
3791 6164 0.900421 TGACAGGCTCTGGAGATGTG 59.100 55.000 11.66 4.10 35.51 3.21
3796 6169 0.972134 TGTCTTGACAGGCTCTGGAG 59.028 55.000 0.00 0.00 35.51 3.86
3798 6171 0.683973 AGTGTCTTGACAGGCTCTGG 59.316 55.000 3.45 0.00 35.51 3.86
3799 6172 3.243873 TGTTAGTGTCTTGACAGGCTCTG 60.244 47.826 3.45 1.16 37.52 3.35
3800 6173 2.965831 TGTTAGTGTCTTGACAGGCTCT 59.034 45.455 3.45 0.87 33.09 4.09
3801 6174 3.243907 ACTGTTAGTGTCTTGACAGGCTC 60.244 47.826 3.45 0.00 42.81 4.70
3802 6175 2.700897 ACTGTTAGTGTCTTGACAGGCT 59.299 45.455 3.45 1.89 42.81 4.58
3803 6176 3.113260 ACTGTTAGTGTCTTGACAGGC 57.887 47.619 3.45 0.00 42.81 4.85
3804 6177 5.844004 AGTAACTGTTAGTGTCTTGACAGG 58.156 41.667 7.09 0.00 42.81 4.00
3805 6178 8.136165 AGTAAGTAACTGTTAGTGTCTTGACAG 58.864 37.037 8.57 0.00 43.81 3.51
3806 6179 8.004087 AGTAAGTAACTGTTAGTGTCTTGACA 57.996 34.615 8.57 0.00 36.93 3.58
3807 6180 8.351461 AGAGTAAGTAACTGTTAGTGTCTTGAC 58.649 37.037 8.57 0.00 39.07 3.18
3808 6181 8.461249 AGAGTAAGTAACTGTTAGTGTCTTGA 57.539 34.615 8.57 0.00 39.07 3.02
3809 6182 7.534578 CGAGAGTAAGTAACTGTTAGTGTCTTG 59.465 40.741 8.57 10.50 39.07 3.02
3810 6183 7.443575 TCGAGAGTAAGTAACTGTTAGTGTCTT 59.556 37.037 8.57 7.35 39.07 3.01
3811 6184 6.933521 TCGAGAGTAAGTAACTGTTAGTGTCT 59.066 38.462 8.57 10.55 39.07 3.41
3812 6185 7.126726 TCGAGAGTAAGTAACTGTTAGTGTC 57.873 40.000 8.57 6.61 39.07 3.67
3813 6186 7.502120 TTCGAGAGTAAGTAACTGTTAGTGT 57.498 36.000 8.57 2.94 39.07 3.55
3814 6187 7.060864 GCTTTCGAGAGTAAGTAACTGTTAGTG 59.939 40.741 8.57 0.00 40.19 2.74
3822 6195 4.422840 GGAGGCTTTCGAGAGTAAGTAAC 58.577 47.826 4.73 0.00 40.19 2.50
3828 6201 1.285373 AGAGGGAGGCTTTCGAGAGTA 59.715 52.381 4.73 0.00 0.00 2.59
3829 6202 0.040499 AGAGGGAGGCTTTCGAGAGT 59.960 55.000 4.73 0.00 0.00 3.24
3831 6204 1.564818 TCTAGAGGGAGGCTTTCGAGA 59.435 52.381 0.00 0.00 0.00 4.04
3832 6205 1.953686 CTCTAGAGGGAGGCTTTCGAG 59.046 57.143 12.27 0.00 0.00 4.04
3833 6206 1.410365 CCTCTAGAGGGAGGCTTTCGA 60.410 57.143 28.68 0.00 45.07 3.71
3834 6207 1.036707 CCTCTAGAGGGAGGCTTTCG 58.963 60.000 28.68 1.06 45.07 3.46
3854 6227 3.873952 ACTTTGAAGACAAGAGCTGTGAC 59.126 43.478 0.00 0.00 38.84 3.67
3855 6228 4.142609 ACTTTGAAGACAAGAGCTGTGA 57.857 40.909 0.00 0.00 38.84 3.58
3856 6229 4.574013 AGAACTTTGAAGACAAGAGCTGTG 59.426 41.667 0.00 0.00 38.84 3.66
3858 6231 5.747951 AAGAACTTTGAAGACAAGAGCTG 57.252 39.130 0.00 0.00 37.32 4.24
3873 6246 5.184287 TCGTTGGAAAGAAACCAAAGAACTT 59.816 36.000 11.45 0.00 46.54 2.66
3874 6247 4.703093 TCGTTGGAAAGAAACCAAAGAACT 59.297 37.500 11.45 0.00 46.54 3.01
3875 6248 4.989044 TCGTTGGAAAGAAACCAAAGAAC 58.011 39.130 11.45 0.00 46.54 3.01
3878 6251 5.696260 GTTTCGTTGGAAAGAAACCAAAG 57.304 39.130 15.78 0.00 46.77 2.77
3884 6257 2.478200 GGCACGTTTCGTTGGAAAGAAA 60.478 45.455 0.00 0.00 42.54 2.52
3885 6258 1.064357 GGCACGTTTCGTTGGAAAGAA 59.936 47.619 0.00 0.00 42.54 2.52
3891 6267 1.729131 GCATGGCACGTTTCGTTGG 60.729 57.895 0.00 0.00 38.32 3.77
3894 6270 0.387112 CATTGCATGGCACGTTTCGT 60.387 50.000 0.00 0.00 38.71 3.85
3896 6272 0.666880 TGCATTGCATGGCACGTTTC 60.667 50.000 7.38 0.00 38.71 2.78
3944 6320 3.194968 GGAACAATCTCTACAACGAGGGA 59.805 47.826 0.00 0.00 0.00 4.20
3947 6323 3.852536 GTCGGAACAATCTCTACAACGAG 59.147 47.826 0.00 0.00 0.00 4.18
3955 6346 3.594603 AACATCGTCGGAACAATCTCT 57.405 42.857 0.00 0.00 0.00 3.10
3957 6348 2.742053 CCAAACATCGTCGGAACAATCT 59.258 45.455 0.00 0.00 0.00 2.40
3959 6350 1.810151 CCCAAACATCGTCGGAACAAT 59.190 47.619 0.00 0.00 0.00 2.71
3974 6365 5.726308 TCAGATCCTCTTATGAGAACCCAAA 59.274 40.000 7.19 0.00 42.73 3.28
3976 6367 4.883759 TCAGATCCTCTTATGAGAACCCA 58.116 43.478 7.19 0.00 42.73 4.51
3977 6368 5.878406 TTCAGATCCTCTTATGAGAACCC 57.122 43.478 7.19 0.00 42.73 4.11
3981 6372 6.212388 GGGCTTATTCAGATCCTCTTATGAGA 59.788 42.308 7.19 0.00 42.73 3.27
3982 6373 6.405538 GGGCTTATTCAGATCCTCTTATGAG 58.594 44.000 0.00 0.00 39.92 2.90
3983 6374 5.249393 GGGGCTTATTCAGATCCTCTTATGA 59.751 44.000 0.00 0.00 0.00 2.15
3984 6375 5.013495 TGGGGCTTATTCAGATCCTCTTATG 59.987 44.000 0.00 0.00 0.00 1.90
3993 6953 4.043812 AGCATGTATGGGGCTTATTCAGAT 59.956 41.667 0.00 0.00 33.21 2.90
4027 6987 1.264045 TGCACATCATCCGGGACTGA 61.264 55.000 0.00 5.26 0.00 3.41
4089 7049 2.824341 CAAAAGAGAGGCTGGCTGAAAT 59.176 45.455 9.06 0.00 0.00 2.17
4090 7050 2.233271 CAAAAGAGAGGCTGGCTGAAA 58.767 47.619 9.06 0.00 0.00 2.69
4094 7054 2.553247 GGTTACAAAAGAGAGGCTGGCT 60.553 50.000 2.24 2.24 0.00 4.75
4117 7077 5.104259 AGGTGAAATTCTTTCTAGCGGAT 57.896 39.130 0.00 0.00 40.32 4.18
4172 7149 0.327924 TCACAACCCTATGCCACAGG 59.672 55.000 0.00 0.00 0.00 4.00
4186 7163 4.038883 TGATGTGCAATTCATTGGTCACAA 59.961 37.500 13.57 0.00 41.03 3.33
4244 7221 1.471501 CCTTTCCGACATCGATGCTCA 60.472 52.381 25.11 4.11 43.02 4.26
4252 7229 3.751698 AGCAAGTTAACCTTTCCGACATC 59.248 43.478 0.88 0.00 0.00 3.06
4256 7233 3.478857 TCAGCAAGTTAACCTTTCCGA 57.521 42.857 0.88 0.00 0.00 4.55
4380 7374 2.841442 AACCTCGAGGAAAAGACTGG 57.159 50.000 37.69 8.57 38.94 4.00
4391 7385 0.040067 GTGCTTGCCAAAACCTCGAG 60.040 55.000 5.13 5.13 0.00 4.04
4399 7393 3.294493 GCTCCCGTGCTTGCCAAA 61.294 61.111 0.00 0.00 0.00 3.28
4410 7404 1.523258 CCTGCTGAGATTGCTCCCG 60.523 63.158 0.00 0.00 40.55 5.14
4429 7423 5.279910 GGAAAGATGGATAGATGGTCAGGAG 60.280 48.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.