Multiple sequence alignment - TraesCS1D01G302300

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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 TraesCS1D01G302300 chr1D 100.000 2294 0 0 1 2294 400060112 400062405 0 4237
1 TraesCS1D01G302300 chr1A 89.082 2125 136 43 205 2294 496476066 496478129 0 2551
2 TraesCS1D01G302300 chr1B 93.991 466 21 5 175 635 536769751 536770214 0 699
3 TraesCS1D01G302300 chr1B 85.693 678 35 25 766 1399 536770433 536771092 0 658


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 TraesCS1D01G302300 chr1D 400060112 400062405 2293 False 4237.0 4237 100.000 1 2294 1 chr1D.!!$F1 2293
1 TraesCS1D01G302300 chr1A 496476066 496478129 2063 False 2551.0 2551 89.082 205 2294 1 chr1A.!!$F1 2089
2 TraesCS1D01G302300 chr1B 536769751 536771092 1341 False 678.5 699 89.842 175 1399 2 chr1B.!!$F1 1224

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
621 632 0.03582 GGGAGTGGGCGTCAACATTA 60.036 55.0 0.0 0.0 0.0 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 1901 0.109412 ATTGCAAAAGAGCTGAGCGC 60.109 50.0 1.71 0.0 39.57 5.92 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
17 18 2.050985 GTGCGTTTGCTGTCTGCC 60.051 61.111 0.00 0.00 43.34 4.85
18 19 2.203195 TGCGTTTGCTGTCTGCCT 60.203 55.556 0.00 0.00 43.34 4.75
19 20 1.823470 TGCGTTTGCTGTCTGCCTT 60.823 52.632 0.00 0.00 43.34 4.35
20 21 1.370900 GCGTTTGCTGTCTGCCTTG 60.371 57.895 0.00 0.00 42.00 3.61
21 22 1.785041 GCGTTTGCTGTCTGCCTTGA 61.785 55.000 0.00 0.00 42.00 3.02
22 23 0.040958 CGTTTGCTGTCTGCCTTGAC 60.041 55.000 0.00 0.00 42.00 3.18
23 24 0.312102 GTTTGCTGTCTGCCTTGACC 59.688 55.000 0.00 0.00 42.00 4.02
24 25 0.823356 TTTGCTGTCTGCCTTGACCC 60.823 55.000 0.00 0.00 42.00 4.46
25 26 1.993701 TTGCTGTCTGCCTTGACCCA 61.994 55.000 0.00 0.00 42.00 4.51
26 27 1.228245 GCTGTCTGCCTTGACCCAA 60.228 57.895 0.00 0.00 36.21 4.12
27 28 0.823356 GCTGTCTGCCTTGACCCAAA 60.823 55.000 0.00 0.00 36.21 3.28
28 29 0.954452 CTGTCTGCCTTGACCCAAAC 59.046 55.000 0.00 0.00 36.21 2.93
29 30 0.467290 TGTCTGCCTTGACCCAAACC 60.467 55.000 0.00 0.00 36.21 3.27
30 31 1.228124 TCTGCCTTGACCCAAACCG 60.228 57.895 0.00 0.00 0.00 4.44
31 32 1.228124 CTGCCTTGACCCAAACCGA 60.228 57.895 0.00 0.00 0.00 4.69
32 33 1.228124 TGCCTTGACCCAAACCGAG 60.228 57.895 0.00 0.00 0.00 4.63
33 34 2.626780 GCCTTGACCCAAACCGAGC 61.627 63.158 0.00 0.00 0.00 5.03
34 35 2.325082 CCTTGACCCAAACCGAGCG 61.325 63.158 0.00 0.00 0.00 5.03
35 36 2.966309 CTTGACCCAAACCGAGCGC 61.966 63.158 0.00 0.00 0.00 5.92
36 37 3.758973 TTGACCCAAACCGAGCGCA 62.759 57.895 11.47 0.00 0.00 6.09
37 38 2.746277 GACCCAAACCGAGCGCAT 60.746 61.111 11.47 0.00 0.00 4.73
38 39 3.039202 GACCCAAACCGAGCGCATG 62.039 63.158 11.47 0.00 0.00 4.06
39 40 3.055719 CCCAAACCGAGCGCATGT 61.056 61.111 11.47 0.00 0.00 3.21
40 41 2.625823 CCCAAACCGAGCGCATGTT 61.626 57.895 11.47 6.80 0.00 2.71
41 42 1.285641 CCAAACCGAGCGCATGTTT 59.714 52.632 11.47 13.00 32.70 2.83
42 43 1.003262 CCAAACCGAGCGCATGTTTG 61.003 55.000 27.99 27.99 45.18 2.93
43 44 1.371635 AAACCGAGCGCATGTTTGC 60.372 52.632 11.47 0.00 45.78 3.68
54 55 3.172000 GCATGTTTGCGTTCAAAATGG 57.828 42.857 0.00 0.00 43.12 3.16
55 56 2.799412 GCATGTTTGCGTTCAAAATGGA 59.201 40.909 0.00 0.00 43.12 3.41
56 57 3.432933 GCATGTTTGCGTTCAAAATGGAT 59.567 39.130 0.00 0.00 43.12 3.41
57 58 4.434593 GCATGTTTGCGTTCAAAATGGATC 60.435 41.667 0.00 0.00 43.12 3.36
58 59 4.313277 TGTTTGCGTTCAAAATGGATCA 57.687 36.364 0.00 0.00 43.12 2.92
59 60 4.297510 TGTTTGCGTTCAAAATGGATCAG 58.702 39.130 0.00 0.00 43.12 2.90
60 61 3.574284 TTGCGTTCAAAATGGATCAGG 57.426 42.857 0.00 0.00 0.00 3.86
61 62 1.202114 TGCGTTCAAAATGGATCAGGC 59.798 47.619 0.00 0.00 0.00 4.85
62 63 1.469767 GCGTTCAAAATGGATCAGGCC 60.470 52.381 0.00 0.00 0.00 5.19
63 64 1.818060 CGTTCAAAATGGATCAGGCCA 59.182 47.619 5.01 0.00 43.23 5.36
64 65 2.230992 CGTTCAAAATGGATCAGGCCAA 59.769 45.455 5.01 0.00 42.16 4.52
65 66 3.305950 CGTTCAAAATGGATCAGGCCAAA 60.306 43.478 5.01 0.00 42.16 3.28
66 67 3.959535 TCAAAATGGATCAGGCCAAAC 57.040 42.857 5.01 0.00 42.16 2.93
67 68 3.237746 TCAAAATGGATCAGGCCAAACA 58.762 40.909 5.01 0.00 42.16 2.83
68 69 3.006752 TCAAAATGGATCAGGCCAAACAC 59.993 43.478 5.01 0.00 42.16 3.32
69 70 2.307496 AATGGATCAGGCCAAACACA 57.693 45.000 5.01 0.00 42.16 3.72
70 71 2.307496 ATGGATCAGGCCAAACACAA 57.693 45.000 5.01 0.00 42.16 3.33
71 72 2.079170 TGGATCAGGCCAAACACAAA 57.921 45.000 5.01 0.00 34.31 2.83
72 73 2.392662 TGGATCAGGCCAAACACAAAA 58.607 42.857 5.01 0.00 34.31 2.44
73 74 2.102252 TGGATCAGGCCAAACACAAAAC 59.898 45.455 5.01 0.00 34.31 2.43
74 75 2.393764 GATCAGGCCAAACACAAAACG 58.606 47.619 5.01 0.00 0.00 3.60
75 76 1.464734 TCAGGCCAAACACAAAACGA 58.535 45.000 5.01 0.00 0.00 3.85
76 77 1.819288 TCAGGCCAAACACAAAACGAA 59.181 42.857 5.01 0.00 0.00 3.85
77 78 1.923864 CAGGCCAAACACAAAACGAAC 59.076 47.619 5.01 0.00 0.00 3.95
78 79 1.546476 AGGCCAAACACAAAACGAACA 59.454 42.857 5.01 0.00 0.00 3.18
79 80 2.028930 AGGCCAAACACAAAACGAACAA 60.029 40.909 5.01 0.00 0.00 2.83
80 81 2.347150 GGCCAAACACAAAACGAACAAG 59.653 45.455 0.00 0.00 0.00 3.16
81 82 3.246619 GCCAAACACAAAACGAACAAGA 58.753 40.909 0.00 0.00 0.00 3.02
82 83 3.862845 GCCAAACACAAAACGAACAAGAT 59.137 39.130 0.00 0.00 0.00 2.40
83 84 4.259770 GCCAAACACAAAACGAACAAGATG 60.260 41.667 0.00 0.00 0.00 2.90
84 85 4.267452 CCAAACACAAAACGAACAAGATGG 59.733 41.667 0.00 0.00 0.00 3.51
85 86 3.708563 ACACAAAACGAACAAGATGGG 57.291 42.857 0.00 0.00 0.00 4.00
86 87 3.020984 ACACAAAACGAACAAGATGGGT 58.979 40.909 0.00 0.00 0.00 4.51
87 88 3.445805 ACACAAAACGAACAAGATGGGTT 59.554 39.130 0.00 0.00 0.00 4.11
88 89 4.041723 CACAAAACGAACAAGATGGGTTC 58.958 43.478 0.00 0.00 40.89 3.62
89 90 3.697045 ACAAAACGAACAAGATGGGTTCA 59.303 39.130 6.16 0.00 43.70 3.18
90 91 4.202010 ACAAAACGAACAAGATGGGTTCAG 60.202 41.667 6.16 2.11 43.70 3.02
91 92 2.185004 ACGAACAAGATGGGTTCAGG 57.815 50.000 6.16 0.00 43.70 3.86
92 93 0.804989 CGAACAAGATGGGTTCAGGC 59.195 55.000 6.16 0.00 43.70 4.85
93 94 1.177401 GAACAAGATGGGTTCAGGCC 58.823 55.000 0.00 0.00 43.16 5.19
94 95 0.609131 AACAAGATGGGTTCAGGCCG 60.609 55.000 0.00 0.00 0.00 6.13
95 96 1.002134 CAAGATGGGTTCAGGCCGT 60.002 57.895 0.00 0.00 0.00 5.68
96 97 1.026718 CAAGATGGGTTCAGGCCGTC 61.027 60.000 0.00 0.00 0.00 4.79
97 98 2.511600 GATGGGTTCAGGCCGTCG 60.512 66.667 0.00 0.00 0.00 5.12
98 99 4.778143 ATGGGTTCAGGCCGTCGC 62.778 66.667 0.00 0.00 0.00 5.19
119 120 4.265056 GTTGGCCGTGGGGTCTGT 62.265 66.667 0.00 0.00 39.29 3.41
120 121 3.494254 TTGGCCGTGGGGTCTGTT 61.494 61.111 0.00 0.00 39.29 3.16
121 122 3.485346 TTGGCCGTGGGGTCTGTTC 62.485 63.158 0.00 0.00 39.29 3.18
122 123 3.948719 GGCCGTGGGGTCTGTTCA 61.949 66.667 0.00 0.00 34.09 3.18
123 124 2.351276 GCCGTGGGGTCTGTTCAT 59.649 61.111 0.00 0.00 34.97 2.57
124 125 1.303317 GCCGTGGGGTCTGTTCATT 60.303 57.895 0.00 0.00 34.97 2.57
125 126 0.893727 GCCGTGGGGTCTGTTCATTT 60.894 55.000 0.00 0.00 34.97 2.32
126 127 1.616159 CCGTGGGGTCTGTTCATTTT 58.384 50.000 0.00 0.00 0.00 1.82
127 128 1.269448 CCGTGGGGTCTGTTCATTTTG 59.731 52.381 0.00 0.00 0.00 2.44
128 129 1.335872 CGTGGGGTCTGTTCATTTTGC 60.336 52.381 0.00 0.00 0.00 3.68
129 130 1.000843 GTGGGGTCTGTTCATTTTGCC 59.999 52.381 0.00 0.00 0.00 4.52
130 131 0.608130 GGGGTCTGTTCATTTTGCCC 59.392 55.000 0.00 0.00 0.00 5.36
131 132 1.337118 GGGTCTGTTCATTTTGCCCA 58.663 50.000 0.00 0.00 34.95 5.36
132 133 1.691434 GGGTCTGTTCATTTTGCCCAA 59.309 47.619 0.00 0.00 34.95 4.12
133 134 2.103941 GGGTCTGTTCATTTTGCCCAAA 59.896 45.455 0.00 0.00 34.95 3.28
134 135 3.130633 GGTCTGTTCATTTTGCCCAAAC 58.869 45.455 0.00 0.00 0.00 2.93
135 136 3.431486 GGTCTGTTCATTTTGCCCAAACA 60.431 43.478 0.00 0.00 0.00 2.83
136 137 3.803778 GTCTGTTCATTTTGCCCAAACAG 59.196 43.478 7.12 7.12 45.10 3.16
137 138 4.057406 CTGTTCATTTTGCCCAAACAGA 57.943 40.909 7.58 0.00 46.09 3.41
138 139 3.791245 TGTTCATTTTGCCCAAACAGAC 58.209 40.909 0.00 0.00 0.00 3.51
139 140 2.791383 TCATTTTGCCCAAACAGACG 57.209 45.000 0.00 0.00 0.00 4.18
140 141 2.302260 TCATTTTGCCCAAACAGACGA 58.698 42.857 0.00 0.00 0.00 4.20
141 142 2.293122 TCATTTTGCCCAAACAGACGAG 59.707 45.455 0.00 0.00 0.00 4.18
142 143 2.045561 TTTTGCCCAAACAGACGAGA 57.954 45.000 0.00 0.00 0.00 4.04
143 144 1.305201 TTTGCCCAAACAGACGAGAC 58.695 50.000 0.00 0.00 0.00 3.36
144 145 0.534203 TTGCCCAAACAGACGAGACC 60.534 55.000 0.00 0.00 0.00 3.85
145 146 2.027625 GCCCAAACAGACGAGACCG 61.028 63.158 0.00 0.00 42.50 4.79
146 147 1.374252 CCCAAACAGACGAGACCGG 60.374 63.158 0.00 0.00 40.78 5.28
147 148 1.663739 CCAAACAGACGAGACCGGA 59.336 57.895 9.46 0.00 40.78 5.14
148 149 0.666577 CCAAACAGACGAGACCGGAC 60.667 60.000 9.46 0.10 40.78 4.79
149 150 1.002250 CAAACAGACGAGACCGGACG 61.002 60.000 9.46 13.68 40.78 4.79
150 151 2.138656 AAACAGACGAGACCGGACGG 62.139 60.000 9.46 9.56 40.78 4.79
151 152 3.812019 CAGACGAGACCGGACGGG 61.812 72.222 9.46 6.67 40.78 5.28
152 153 4.025858 AGACGAGACCGGACGGGA 62.026 66.667 9.46 0.00 40.78 5.14
153 154 2.827642 GACGAGACCGGACGGGAT 60.828 66.667 9.46 2.52 40.78 3.85
154 155 3.122250 GACGAGACCGGACGGGATG 62.122 68.421 9.46 4.53 40.78 3.51
155 156 3.900892 CGAGACCGGACGGGATGG 61.901 72.222 9.46 0.60 39.97 3.51
156 157 2.441532 GAGACCGGACGGGATGGA 60.442 66.667 9.46 0.00 39.97 3.41
157 158 2.442272 AGACCGGACGGGATGGAG 60.442 66.667 9.46 0.00 39.97 3.86
158 159 2.758737 GACCGGACGGGATGGAGT 60.759 66.667 9.46 0.00 39.97 3.85
159 160 2.758737 ACCGGACGGGATGGAGTC 60.759 66.667 9.46 0.00 39.97 3.36
160 161 3.900892 CCGGACGGGATGGAGTCG 61.901 72.222 0.00 0.00 38.47 4.18
161 162 4.570663 CGGACGGGATGGAGTCGC 62.571 72.222 0.00 0.00 38.20 5.19
167 168 4.492160 GGATGGAGTCGCGCGTGA 62.492 66.667 30.98 20.10 0.00 4.35
168 169 2.506217 GATGGAGTCGCGCGTGAA 60.506 61.111 30.98 9.35 0.00 3.18
169 170 1.878522 GATGGAGTCGCGCGTGAAT 60.879 57.895 30.98 24.73 0.00 2.57
170 171 2.082437 GATGGAGTCGCGCGTGAATG 62.082 60.000 28.38 0.00 0.00 2.67
171 172 3.554692 GGAGTCGCGCGTGAATGG 61.555 66.667 28.38 0.00 0.00 3.16
172 173 2.506217 GAGTCGCGCGTGAATGGA 60.506 61.111 28.38 5.11 0.00 3.41
173 174 2.507102 AGTCGCGCGTGAATGGAG 60.507 61.111 30.98 0.00 0.00 3.86
213 214 7.568199 ACTACGATGGGAAAATAAAATGAGG 57.432 36.000 0.00 0.00 0.00 3.86
244 248 1.202903 ACTACTACAGGATCCCGCGAT 60.203 52.381 8.23 0.00 0.00 4.58
252 256 1.741770 GATCCCGCGATGGCATACC 60.742 63.158 8.23 0.00 39.92 2.73
324 332 3.665675 CTCCCGGCCCGAGACAAAG 62.666 68.421 3.71 0.00 0.00 2.77
455 463 1.909302 CCCTTGTCACCCACAGTATCT 59.091 52.381 0.00 0.00 35.97 1.98
470 478 3.389656 CAGTATCTCCCCTCCTCCTTTTC 59.610 52.174 0.00 0.00 0.00 2.29
572 582 4.528674 GCTGATGAGCACGACCAT 57.471 55.556 0.00 0.00 45.46 3.55
610 621 2.162681 GTTGACATTCTTGGGAGTGGG 58.837 52.381 0.00 0.00 34.13 4.61
612 623 1.002134 ACATTCTTGGGAGTGGGCG 60.002 57.895 0.00 0.00 34.13 6.13
613 624 1.002134 CATTCTTGGGAGTGGGCGT 60.002 57.895 0.00 0.00 0.00 5.68
621 632 0.035820 GGGAGTGGGCGTCAACATTA 60.036 55.000 0.00 0.00 0.00 1.90
622 633 1.084289 GGAGTGGGCGTCAACATTAC 58.916 55.000 0.00 0.00 0.00 1.89
632 643 5.514914 GGGCGTCAACATTACATACAAATTG 59.485 40.000 0.00 0.00 0.00 2.32
716 765 9.921637 TTTTAGCCGAAAACATATTCAGATTTT 57.078 25.926 0.00 0.00 31.90 1.82
717 766 9.921637 TTTAGCCGAAAACATATTCAGATTTTT 57.078 25.926 0.00 0.00 0.00 1.94
743 792 8.783833 TTGAGGAGTATTCAGATTTTCTTCTG 57.216 34.615 0.00 0.00 43.70 3.02
759 849 3.820467 TCTTCTGTGACGCCATTTTCAAT 59.180 39.130 0.00 0.00 0.00 2.57
762 852 2.988493 CTGTGACGCCATTTTCAATTGG 59.012 45.455 5.42 0.00 36.03 3.16
765 855 2.230992 TGACGCCATTTTCAATTGGAGG 59.769 45.455 5.42 0.00 37.15 4.30
781 871 1.341089 GGAGGAAACCCTGACCCATTC 60.341 57.143 0.00 0.00 33.25 2.67
782 872 0.328258 AGGAAACCCTGACCCATTCG 59.672 55.000 0.00 0.00 31.48 3.34
783 873 0.037734 GGAAACCCTGACCCATTCGT 59.962 55.000 0.00 0.00 0.00 3.85
785 875 2.290450 GGAAACCCTGACCCATTCGTAA 60.290 50.000 0.00 0.00 0.00 3.18
834 951 3.981308 CAATTTCTGGACCGCCGT 58.019 55.556 0.00 0.00 36.79 5.68
944 1080 2.278466 AGCTCGCGAATCTGCTCG 60.278 61.111 14.12 0.00 41.84 5.03
953 1089 2.867333 GAATCTGCTCGTCGTCGCCA 62.867 60.000 0.00 0.00 36.96 5.69
955 1091 2.669808 ATCTGCTCGTCGTCGCCATC 62.670 60.000 0.00 0.00 36.96 3.51
956 1092 4.492160 TGCTCGTCGTCGCCATCC 62.492 66.667 0.00 0.00 36.96 3.51
958 1094 4.570663 CTCGTCGTCGCCATCCCC 62.571 72.222 0.00 0.00 36.96 4.81
1143 1295 1.037579 CGCTCCCTTTCCCCATTTCC 61.038 60.000 0.00 0.00 0.00 3.13
1303 1464 1.523938 GCCAACTAGGTGCGGATCC 60.524 63.158 0.87 0.00 40.61 3.36
1315 1476 2.046892 GGATCCGATCCCATGCCG 60.047 66.667 15.75 0.00 43.88 5.69
1340 1517 2.164393 CCTCTTGGGTTTCTGGGGT 58.836 57.895 0.00 0.00 0.00 4.95
1343 1520 1.003696 CTCTTGGGTTTCTGGGGTCTC 59.996 57.143 0.00 0.00 0.00 3.36
1351 1528 2.681778 CTGGGGTCTCGGCTCTGT 60.682 66.667 0.00 0.00 0.00 3.41
1358 1535 1.634702 GTCTCGGCTCTGTGATGAAC 58.365 55.000 0.00 0.00 0.00 3.18
1372 1549 4.349636 TGTGATGAACTTCTAGGGTTTGGA 59.650 41.667 0.00 0.00 0.00 3.53
1374 1551 3.782656 TGAACTTCTAGGGTTTGGACC 57.217 47.619 0.00 0.00 45.75 4.46
1382 1559 3.039134 GGTTTGGACCGCTGTTGG 58.961 61.111 0.00 0.00 35.91 3.77
1393 1570 2.835764 ACCGCTGTTGGGTTAGAATAGA 59.164 45.455 0.00 0.00 32.70 1.98
1399 1576 5.743422 GCTGTTGGGTTAGAATAGATCCCTC 60.743 48.000 0.00 0.00 38.95 4.30
1400 1577 5.538877 TGTTGGGTTAGAATAGATCCCTCT 58.461 41.667 0.00 0.00 38.95 3.69
1401 1578 5.970640 TGTTGGGTTAGAATAGATCCCTCTT 59.029 40.000 0.00 0.00 38.95 2.85
1411 1588 3.160679 AGATCCCTCTTTGTTGTTGGG 57.839 47.619 0.00 0.00 39.22 4.12
1424 1601 2.684374 GTTGTTGGGTACGAGGTGTTTT 59.316 45.455 0.00 0.00 0.00 2.43
1450 1627 2.579400 GGGGGTTACTAATTGGGAGTGT 59.421 50.000 0.00 0.00 0.00 3.55
1454 1631 3.939592 GGTTACTAATTGGGAGTGTCTGC 59.060 47.826 0.00 0.00 0.00 4.26
1484 1661 1.746615 GCATTTCTCCGCAGCTGGA 60.747 57.895 17.12 3.96 36.37 3.86
1490 1667 3.982316 CTCCGCAGCTGGATTGCCA 62.982 63.158 17.12 0.00 43.47 4.92
1516 1693 1.128692 GATTGGTAGTGCGTTGCAGAC 59.871 52.381 0.00 0.00 40.08 3.51
1531 1708 0.244994 CAGACCACTGGAGACTTCGG 59.755 60.000 0.71 0.00 40.14 4.30
1565 1742 4.168760 GTCATGTTTGGCTGTTATGCTTC 58.831 43.478 0.00 0.00 0.00 3.86
1597 1774 2.620251 TTGCAGTGTGCTAGACTTGT 57.380 45.000 0.00 0.00 45.31 3.16
1598 1775 3.744238 TTGCAGTGTGCTAGACTTGTA 57.256 42.857 0.00 0.00 45.31 2.41
1599 1776 3.026630 TGCAGTGTGCTAGACTTGTAC 57.973 47.619 0.00 0.00 45.31 2.90
1600 1777 2.364002 TGCAGTGTGCTAGACTTGTACA 59.636 45.455 3.89 3.89 45.31 2.90
1601 1778 3.181470 TGCAGTGTGCTAGACTTGTACAA 60.181 43.478 8.28 8.28 45.31 2.41
1602 1779 3.997021 GCAGTGTGCTAGACTTGTACAAT 59.003 43.478 9.13 5.90 40.96 2.71
1603 1780 4.452455 GCAGTGTGCTAGACTTGTACAATT 59.548 41.667 9.13 2.95 40.96 2.32
1604 1781 5.615544 GCAGTGTGCTAGACTTGTACAATTG 60.616 44.000 9.13 3.24 40.96 2.32
1622 1799 9.559958 GTACAATTGTACTGGATTTCTGATTTG 57.440 33.333 32.21 0.00 45.47 2.32
1633 1810 7.004086 TGGATTTCTGATTTGGTTGTTACTCT 58.996 34.615 0.00 0.00 0.00 3.24
1634 1811 8.160765 TGGATTTCTGATTTGGTTGTTACTCTA 58.839 33.333 0.00 0.00 0.00 2.43
1635 1812 9.178758 GGATTTCTGATTTGGTTGTTACTCTAT 57.821 33.333 0.00 0.00 0.00 1.98
1636 1813 9.994432 GATTTCTGATTTGGTTGTTACTCTATG 57.006 33.333 0.00 0.00 0.00 2.23
1660 1837 3.299503 AGCCCCATTTTCGCTATCAAAT 58.700 40.909 0.00 0.00 0.00 2.32
1668 1845 7.424803 CCATTTTCGCTATCAAATTGATGGTA 58.575 34.615 17.93 5.72 37.62 3.25
1684 1861 0.881796 GGTACAGCTTGGGTTCTTGC 59.118 55.000 0.00 0.00 0.00 4.01
1701 1878 6.128117 GGTTCTTGCGGTATTTGAATGTAAGA 60.128 38.462 0.00 0.00 0.00 2.10
1718 1895 9.989869 GAATGTAAGACTAGTTTAGAAAATGGC 57.010 33.333 0.00 0.00 0.00 4.40
1724 1901 4.631813 ACTAGTTTAGAAAATGGCAGAGCG 59.368 41.667 0.00 0.00 0.00 5.03
1726 1903 0.726827 TTAGAAAATGGCAGAGCGCG 59.273 50.000 0.00 0.00 43.84 6.86
1727 1904 1.705337 TAGAAAATGGCAGAGCGCGC 61.705 55.000 26.66 26.66 43.84 6.86
1728 1905 3.044059 GAAAATGGCAGAGCGCGCT 62.044 57.895 37.28 37.28 43.84 5.92
1729 1906 2.909762 GAAAATGGCAGAGCGCGCTC 62.910 60.000 45.46 45.46 43.84 5.03
1738 1915 2.358003 AGCGCGCTCAGCTCTTTT 60.358 55.556 31.32 0.91 41.83 2.27
1757 1934 4.822685 TTTGCAATGAGGTAAATGCCAT 57.177 36.364 0.00 0.00 38.00 4.40
1772 1949 1.133199 TGCCATCTGGTTGGGTCTTTT 60.133 47.619 0.00 0.00 37.24 2.27
1788 1965 3.045634 TCTTTTGAGGTGGGAGAAGTGA 58.954 45.455 0.00 0.00 0.00 3.41
1822 1999 2.811317 GCGCTTCCTCTGGTCGTG 60.811 66.667 0.00 0.00 0.00 4.35
1825 2002 0.242825 CGCTTCCTCTGGTCGTGTTA 59.757 55.000 0.00 0.00 0.00 2.41
1828 2005 2.738964 GCTTCCTCTGGTCGTGTTATCC 60.739 54.545 0.00 0.00 0.00 2.59
1847 2024 1.466167 CCAGTCATCGCAGTGGAAAAG 59.534 52.381 0.00 0.00 39.02 2.27
1892 2069 2.161211 CAGCTTGCTTTGCCTAGTCTTC 59.839 50.000 0.00 0.00 0.00 2.87
1902 2079 5.489792 TTGCCTAGTCTTCTGAAGAATGT 57.510 39.130 25.59 14.53 39.67 2.71
1955 2134 4.407296 ACTCTCCAATCTCCTGTGAATACC 59.593 45.833 0.00 0.00 0.00 2.73
2042 2221 5.652014 TGATCTTCATGTTACATTGTTCCCC 59.348 40.000 0.00 0.00 0.00 4.81
2076 2255 0.620556 ATCTTGTGATTGCCCGGTCT 59.379 50.000 0.00 0.00 0.00 3.85
2095 2274 6.183360 CCGGTCTATTCTTGTCTTCCTCAATA 60.183 42.308 0.00 0.00 0.00 1.90
2116 2295 4.273148 AGTATTATCCTTCCCGTGCATC 57.727 45.455 0.00 0.00 0.00 3.91
2119 2298 1.046472 TATCCTTCCCGTGCATCCGT 61.046 55.000 0.00 0.00 0.00 4.69
2184 2363 8.185505 TGTTTTAACTGTTTACCACTTCACATC 58.814 33.333 0.00 0.00 0.00 3.06
2190 2369 2.309528 TACCACTTCACATCGGCATC 57.690 50.000 0.00 0.00 0.00 3.91
2197 2376 1.802069 TCACATCGGCATCGTTTGAA 58.198 45.000 0.00 0.00 37.69 2.69
2203 2382 4.335315 ACATCGGCATCGTTTGAACAATAT 59.665 37.500 0.00 0.00 37.69 1.28
2247 2426 5.540911 TCATCTGAAACAATTTTGCCTTCC 58.459 37.500 0.00 0.00 0.00 3.46
2263 2442 1.269723 CTTCCTTTTCCCGTTGCCTTC 59.730 52.381 0.00 0.00 0.00 3.46
2268 2447 0.766131 TTTCCCGTTGCCTTCCTACA 59.234 50.000 0.00 0.00 0.00 2.74
2275 2454 2.616842 CGTTGCCTTCCTACAAACAACT 59.383 45.455 0.00 0.00 36.21 3.16
2284 2463 6.348540 CCTTCCTACAAACAACTGCTATTGAC 60.349 42.308 7.41 0.00 33.57 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.823356 TTTGGGTCAAGGCAGACAGC 60.823 55.000 11.40 0.00 40.29 4.40
9 10 0.954452 GTTTGGGTCAAGGCAGACAG 59.046 55.000 11.40 0.00 40.29 3.51
10 11 0.467290 GGTTTGGGTCAAGGCAGACA 60.467 55.000 11.40 0.00 40.29 3.41
11 12 1.515521 CGGTTTGGGTCAAGGCAGAC 61.516 60.000 1.92 1.92 37.80 3.51
12 13 1.228124 CGGTTTGGGTCAAGGCAGA 60.228 57.895 0.00 0.00 0.00 4.26
13 14 1.228124 TCGGTTTGGGTCAAGGCAG 60.228 57.895 0.00 0.00 0.00 4.85
14 15 1.228124 CTCGGTTTGGGTCAAGGCA 60.228 57.895 0.00 0.00 0.00 4.75
15 16 2.626780 GCTCGGTTTGGGTCAAGGC 61.627 63.158 0.00 0.00 0.00 4.35
16 17 2.325082 CGCTCGGTTTGGGTCAAGG 61.325 63.158 0.00 0.00 0.00 3.61
17 18 2.966309 GCGCTCGGTTTGGGTCAAG 61.966 63.158 0.00 0.00 0.00 3.02
18 19 2.975799 GCGCTCGGTTTGGGTCAA 60.976 61.111 0.00 0.00 0.00 3.18
19 20 3.545124 ATGCGCTCGGTTTGGGTCA 62.545 57.895 9.73 0.00 0.00 4.02
20 21 2.746277 ATGCGCTCGGTTTGGGTC 60.746 61.111 9.73 0.00 0.00 4.46
21 22 3.055719 CATGCGCTCGGTTTGGGT 61.056 61.111 9.73 0.00 0.00 4.51
22 23 2.141122 AAACATGCGCTCGGTTTGGG 62.141 55.000 18.83 0.00 33.78 4.12
23 24 1.003262 CAAACATGCGCTCGGTTTGG 61.003 55.000 28.35 17.60 44.59 3.28
24 25 2.423202 CAAACATGCGCTCGGTTTG 58.577 52.632 25.64 25.64 43.47 2.93
25 26 1.371635 GCAAACATGCGCTCGGTTT 60.372 52.632 9.73 13.44 35.27 3.27
26 27 2.255252 GCAAACATGCGCTCGGTT 59.745 55.556 9.73 7.55 0.00 4.44
34 35 2.799412 TCCATTTTGAACGCAAACATGC 59.201 40.909 0.00 0.00 43.27 4.06
35 36 4.685165 TGATCCATTTTGAACGCAAACATG 59.315 37.500 0.00 0.00 43.27 3.21
36 37 4.880759 TGATCCATTTTGAACGCAAACAT 58.119 34.783 0.00 0.00 43.27 2.71
37 38 4.297510 CTGATCCATTTTGAACGCAAACA 58.702 39.130 0.00 0.00 43.27 2.83
38 39 3.674753 CCTGATCCATTTTGAACGCAAAC 59.325 43.478 0.00 0.00 43.27 2.93
39 40 3.860378 GCCTGATCCATTTTGAACGCAAA 60.860 43.478 0.00 0.00 41.97 3.68
40 41 2.352617 GCCTGATCCATTTTGAACGCAA 60.353 45.455 0.00 0.00 0.00 4.85
41 42 1.202114 GCCTGATCCATTTTGAACGCA 59.798 47.619 0.00 0.00 0.00 5.24
42 43 1.469767 GGCCTGATCCATTTTGAACGC 60.470 52.381 0.00 0.00 0.00 4.84
43 44 1.818060 TGGCCTGATCCATTTTGAACG 59.182 47.619 3.32 0.00 0.00 3.95
44 45 3.959535 TTGGCCTGATCCATTTTGAAC 57.040 42.857 3.32 0.00 35.77 3.18
45 46 3.645212 TGTTTGGCCTGATCCATTTTGAA 59.355 39.130 3.32 0.00 35.77 2.69
46 47 3.006752 GTGTTTGGCCTGATCCATTTTGA 59.993 43.478 3.32 0.00 35.77 2.69
47 48 3.244146 TGTGTTTGGCCTGATCCATTTTG 60.244 43.478 3.32 0.00 35.77 2.44
48 49 2.971330 TGTGTTTGGCCTGATCCATTTT 59.029 40.909 3.32 0.00 35.77 1.82
49 50 2.607499 TGTGTTTGGCCTGATCCATTT 58.393 42.857 3.32 0.00 35.77 2.32
50 51 2.307496 TGTGTTTGGCCTGATCCATT 57.693 45.000 3.32 0.00 35.77 3.16
51 52 2.307496 TTGTGTTTGGCCTGATCCAT 57.693 45.000 3.32 0.00 35.77 3.41
52 53 2.079170 TTTGTGTTTGGCCTGATCCA 57.921 45.000 3.32 0.00 0.00 3.41
53 54 2.754472 GTTTTGTGTTTGGCCTGATCC 58.246 47.619 3.32 0.00 0.00 3.36
54 55 2.034053 TCGTTTTGTGTTTGGCCTGATC 59.966 45.455 3.32 0.00 0.00 2.92
55 56 2.028130 TCGTTTTGTGTTTGGCCTGAT 58.972 42.857 3.32 0.00 0.00 2.90
56 57 1.464734 TCGTTTTGTGTTTGGCCTGA 58.535 45.000 3.32 0.00 0.00 3.86
57 58 1.923864 GTTCGTTTTGTGTTTGGCCTG 59.076 47.619 3.32 0.00 0.00 4.85
58 59 1.546476 TGTTCGTTTTGTGTTTGGCCT 59.454 42.857 3.32 0.00 0.00 5.19
59 60 1.997669 TGTTCGTTTTGTGTTTGGCC 58.002 45.000 0.00 0.00 0.00 5.36
60 61 3.246619 TCTTGTTCGTTTTGTGTTTGGC 58.753 40.909 0.00 0.00 0.00 4.52
61 62 4.267452 CCATCTTGTTCGTTTTGTGTTTGG 59.733 41.667 0.00 0.00 0.00 3.28
62 63 4.267452 CCCATCTTGTTCGTTTTGTGTTTG 59.733 41.667 0.00 0.00 0.00 2.93
63 64 4.081917 ACCCATCTTGTTCGTTTTGTGTTT 60.082 37.500 0.00 0.00 0.00 2.83
64 65 3.445805 ACCCATCTTGTTCGTTTTGTGTT 59.554 39.130 0.00 0.00 0.00 3.32
65 66 3.020984 ACCCATCTTGTTCGTTTTGTGT 58.979 40.909 0.00 0.00 0.00 3.72
66 67 3.708563 ACCCATCTTGTTCGTTTTGTG 57.291 42.857 0.00 0.00 0.00 3.33
67 68 3.697045 TGAACCCATCTTGTTCGTTTTGT 59.303 39.130 0.00 0.00 43.95 2.83
68 69 4.290155 CTGAACCCATCTTGTTCGTTTTG 58.710 43.478 0.00 0.00 43.95 2.44
69 70 3.317993 CCTGAACCCATCTTGTTCGTTTT 59.682 43.478 0.00 0.00 43.95 2.43
70 71 2.884639 CCTGAACCCATCTTGTTCGTTT 59.115 45.455 0.00 0.00 43.95 3.60
71 72 2.504367 CCTGAACCCATCTTGTTCGTT 58.496 47.619 0.00 0.00 43.95 3.85
72 73 1.882352 GCCTGAACCCATCTTGTTCGT 60.882 52.381 0.00 0.00 43.95 3.85
73 74 0.804989 GCCTGAACCCATCTTGTTCG 59.195 55.000 0.00 0.00 43.95 3.95
74 75 1.177401 GGCCTGAACCCATCTTGTTC 58.823 55.000 0.00 0.00 41.91 3.18
75 76 0.609131 CGGCCTGAACCCATCTTGTT 60.609 55.000 0.00 0.00 0.00 2.83
76 77 1.002134 CGGCCTGAACCCATCTTGT 60.002 57.895 0.00 0.00 0.00 3.16
77 78 1.002134 ACGGCCTGAACCCATCTTG 60.002 57.895 0.00 0.00 0.00 3.02
78 79 1.299976 GACGGCCTGAACCCATCTT 59.700 57.895 0.00 0.00 0.00 2.40
79 80 2.990479 GACGGCCTGAACCCATCT 59.010 61.111 0.00 0.00 0.00 2.90
80 81 2.511600 CGACGGCCTGAACCCATC 60.512 66.667 0.00 0.00 0.00 3.51
81 82 4.778143 GCGACGGCCTGAACCCAT 62.778 66.667 0.00 0.00 0.00 4.00
102 103 3.785122 AACAGACCCCACGGCCAAC 62.785 63.158 2.24 0.00 0.00 3.77
103 104 3.485346 GAACAGACCCCACGGCCAA 62.485 63.158 2.24 0.00 0.00 4.52
104 105 3.948719 GAACAGACCCCACGGCCA 61.949 66.667 2.24 0.00 0.00 5.36
105 106 2.764637 AATGAACAGACCCCACGGCC 62.765 60.000 0.00 0.00 0.00 6.13
106 107 0.893727 AAATGAACAGACCCCACGGC 60.894 55.000 0.00 0.00 0.00 5.68
107 108 1.269448 CAAAATGAACAGACCCCACGG 59.731 52.381 0.00 0.00 0.00 4.94
108 109 1.335872 GCAAAATGAACAGACCCCACG 60.336 52.381 0.00 0.00 0.00 4.94
109 110 1.000843 GGCAAAATGAACAGACCCCAC 59.999 52.381 0.00 0.00 0.00 4.61
110 111 1.337118 GGCAAAATGAACAGACCCCA 58.663 50.000 0.00 0.00 0.00 4.96
111 112 0.608130 GGGCAAAATGAACAGACCCC 59.392 55.000 0.00 0.00 0.00 4.95
112 113 1.337118 TGGGCAAAATGAACAGACCC 58.663 50.000 0.00 0.00 36.36 4.46
113 114 3.130633 GTTTGGGCAAAATGAACAGACC 58.869 45.455 0.00 0.00 31.33 3.85
114 115 3.791245 TGTTTGGGCAAAATGAACAGAC 58.209 40.909 0.00 0.00 31.33 3.51
115 116 4.057406 CTGTTTGGGCAAAATGAACAGA 57.943 40.909 8.42 0.00 46.14 3.41
116 117 3.803778 GTCTGTTTGGGCAAAATGAACAG 59.196 43.478 7.93 7.93 45.17 3.16
117 118 3.736433 CGTCTGTTTGGGCAAAATGAACA 60.736 43.478 0.00 0.00 31.33 3.18
118 119 2.794350 CGTCTGTTTGGGCAAAATGAAC 59.206 45.455 0.00 0.00 31.33 3.18
119 120 2.690497 TCGTCTGTTTGGGCAAAATGAA 59.310 40.909 0.00 0.00 31.33 2.57
120 121 2.293122 CTCGTCTGTTTGGGCAAAATGA 59.707 45.455 0.00 0.00 31.33 2.57
121 122 2.293122 TCTCGTCTGTTTGGGCAAAATG 59.707 45.455 0.00 0.00 31.33 2.32
122 123 2.293399 GTCTCGTCTGTTTGGGCAAAAT 59.707 45.455 0.00 0.00 31.33 1.82
123 124 1.673920 GTCTCGTCTGTTTGGGCAAAA 59.326 47.619 0.00 0.00 31.33 2.44
124 125 1.305201 GTCTCGTCTGTTTGGGCAAA 58.695 50.000 0.00 0.00 0.00 3.68
125 126 0.534203 GGTCTCGTCTGTTTGGGCAA 60.534 55.000 0.00 0.00 0.00 4.52
126 127 1.070786 GGTCTCGTCTGTTTGGGCA 59.929 57.895 0.00 0.00 0.00 5.36
127 128 2.027625 CGGTCTCGTCTGTTTGGGC 61.028 63.158 0.00 0.00 0.00 5.36
128 129 1.374252 CCGGTCTCGTCTGTTTGGG 60.374 63.158 0.00 0.00 33.95 4.12
129 130 0.666577 GTCCGGTCTCGTCTGTTTGG 60.667 60.000 0.00 0.00 33.95 3.28
130 131 1.002250 CGTCCGGTCTCGTCTGTTTG 61.002 60.000 0.00 0.00 33.95 2.93
131 132 1.285023 CGTCCGGTCTCGTCTGTTT 59.715 57.895 0.00 0.00 33.95 2.83
132 133 2.623915 CCGTCCGGTCTCGTCTGTT 61.624 63.158 0.00 0.00 33.95 3.16
133 134 3.054503 CCGTCCGGTCTCGTCTGT 61.055 66.667 0.00 0.00 33.95 3.41
134 135 3.812019 CCCGTCCGGTCTCGTCTG 61.812 72.222 0.00 0.00 33.95 3.51
135 136 3.341202 ATCCCGTCCGGTCTCGTCT 62.341 63.158 0.00 0.00 33.95 4.18
136 137 2.827642 ATCCCGTCCGGTCTCGTC 60.828 66.667 0.00 0.00 33.95 4.20
137 138 3.138798 CATCCCGTCCGGTCTCGT 61.139 66.667 0.00 0.00 33.95 4.18
138 139 3.900892 CCATCCCGTCCGGTCTCG 61.901 72.222 0.00 5.39 0.00 4.04
139 140 2.441532 TCCATCCCGTCCGGTCTC 60.442 66.667 0.00 0.00 0.00 3.36
140 141 2.442272 CTCCATCCCGTCCGGTCT 60.442 66.667 0.00 0.00 0.00 3.85
141 142 2.758737 ACTCCATCCCGTCCGGTC 60.759 66.667 0.00 0.00 0.00 4.79
142 143 2.758737 GACTCCATCCCGTCCGGT 60.759 66.667 0.00 0.00 0.00 5.28
143 144 3.900892 CGACTCCATCCCGTCCGG 61.901 72.222 0.00 0.00 0.00 5.14
144 145 4.570663 GCGACTCCATCCCGTCCG 62.571 72.222 0.00 0.00 0.00 4.79
145 146 4.570663 CGCGACTCCATCCCGTCC 62.571 72.222 0.00 0.00 0.00 4.79
150 151 3.982372 TTCACGCGCGACTCCATCC 62.982 63.158 39.36 0.00 0.00 3.51
151 152 1.878522 ATTCACGCGCGACTCCATC 60.879 57.895 39.36 0.00 0.00 3.51
152 153 2.167219 CATTCACGCGCGACTCCAT 61.167 57.895 39.36 17.12 0.00 3.41
153 154 2.809174 CATTCACGCGCGACTCCA 60.809 61.111 39.36 15.48 0.00 3.86
154 155 3.554692 CCATTCACGCGCGACTCC 61.555 66.667 39.36 0.00 0.00 3.85
155 156 2.506217 TCCATTCACGCGCGACTC 60.506 61.111 39.36 0.00 0.00 3.36
156 157 2.507102 CTCCATTCACGCGCGACT 60.507 61.111 39.36 13.15 0.00 4.18
157 158 3.554692 CCTCCATTCACGCGCGAC 61.555 66.667 39.36 0.00 0.00 5.19
158 159 4.812476 CCCTCCATTCACGCGCGA 62.812 66.667 39.36 15.84 0.00 5.87
160 161 3.195698 GACCCTCCATTCACGCGC 61.196 66.667 5.73 0.00 0.00 6.86
161 162 1.811266 CTGACCCTCCATTCACGCG 60.811 63.158 3.53 3.53 0.00 6.01
162 163 2.109126 GCTGACCCTCCATTCACGC 61.109 63.158 0.00 0.00 0.00 5.34
163 164 1.450312 GGCTGACCCTCCATTCACG 60.450 63.158 0.00 0.00 0.00 4.35
164 165 1.994463 AGGCTGACCCTCCATTCAC 59.006 57.895 0.00 0.00 41.21 3.18
165 166 4.587520 AGGCTGACCCTCCATTCA 57.412 55.556 0.00 0.00 41.21 2.57
173 174 1.946081 GTAGTAGTACGAGGCTGACCC 59.054 57.143 0.00 0.00 36.11 4.46
244 248 3.580904 GCGTATCTTCGGTATGCCA 57.419 52.632 0.00 0.00 34.09 4.92
252 256 2.202690 TGCGTGGGCGTATCTTCG 60.203 61.111 0.00 0.00 44.10 3.79
324 332 1.673665 GATGGATGGAGATGGCGCC 60.674 63.158 22.73 22.73 34.13 6.53
397 405 3.383185 CGAAAGCCCCCAAAATATTGCTA 59.617 43.478 0.00 0.00 35.10 3.49
455 463 0.123266 ATGGGAAAAGGAGGAGGGGA 59.877 55.000 0.00 0.00 0.00 4.81
470 478 6.884295 TCTTTTACACTAAACAGGATCATGGG 59.116 38.462 12.66 1.78 0.00 4.00
572 582 3.535629 CTGGAGTTGGGCAGTGCGA 62.536 63.158 9.45 0.00 0.00 5.10
602 613 0.035820 TAATGTTGACGCCCACTCCC 60.036 55.000 0.00 0.00 0.00 4.30
610 621 7.960738 AGTACAATTTGTATGTAATGTTGACGC 59.039 33.333 12.16 0.00 35.05 5.19
716 765 9.799106 AGAAGAAAATCTGAATACTCCTCAAAA 57.201 29.630 0.00 0.00 0.00 2.44
731 780 3.126001 TGGCGTCACAGAAGAAAATCT 57.874 42.857 0.00 0.00 0.00 2.40
732 781 4.425577 AATGGCGTCACAGAAGAAAATC 57.574 40.909 0.00 0.00 0.00 2.17
733 782 4.853924 AAATGGCGTCACAGAAGAAAAT 57.146 36.364 0.00 0.00 0.00 1.82
734 783 4.097135 TGAAAATGGCGTCACAGAAGAAAA 59.903 37.500 0.00 0.00 0.00 2.29
735 784 3.629855 TGAAAATGGCGTCACAGAAGAAA 59.370 39.130 0.00 0.00 0.00 2.52
736 785 3.210227 TGAAAATGGCGTCACAGAAGAA 58.790 40.909 0.00 0.00 0.00 2.52
743 792 3.244976 CTCCAATTGAAAATGGCGTCAC 58.755 45.455 7.12 0.00 36.62 3.67
759 849 0.699577 TGGGTCAGGGTTTCCTCCAA 60.700 55.000 0.00 0.00 42.67 3.53
762 852 1.679032 CGAATGGGTCAGGGTTTCCTC 60.679 57.143 0.00 0.00 42.67 3.71
765 855 2.773993 TACGAATGGGTCAGGGTTTC 57.226 50.000 0.00 0.00 0.00 2.78
804 921 3.347216 CAGAAATTGGATCCTTGACCGT 58.653 45.455 14.23 0.00 0.00 4.83
1122 1274 3.662117 AATGGGGAAAGGGAGCGGC 62.662 63.158 0.00 0.00 0.00 6.53
1143 1295 3.234730 CGGGATTCGGGGGAGAGG 61.235 72.222 0.00 0.00 34.75 3.69
1340 1517 1.550327 AGTTCATCACAGAGCCGAGA 58.450 50.000 0.00 0.00 0.00 4.04
1343 1520 2.376808 AGAAGTTCATCACAGAGCCG 57.623 50.000 5.50 0.00 0.00 5.52
1351 1528 4.263331 GGTCCAAACCCTAGAAGTTCATCA 60.263 45.833 5.50 0.00 39.93 3.07
1358 1535 0.613777 AGCGGTCCAAACCCTAGAAG 59.386 55.000 0.00 0.00 43.21 2.85
1372 1549 2.835764 TCTATTCTAACCCAACAGCGGT 59.164 45.455 0.00 0.00 34.07 5.68
1374 1551 4.058817 GGATCTATTCTAACCCAACAGCG 58.941 47.826 0.00 0.00 0.00 5.18
1376 1553 5.604650 AGAGGGATCTATTCTAACCCAACAG 59.395 44.000 0.00 0.00 42.62 3.16
1381 1558 6.502074 ACAAAGAGGGATCTATTCTAACCC 57.498 41.667 0.00 0.00 40.71 4.11
1382 1559 7.339482 ACAACAAAGAGGGATCTATTCTAACC 58.661 38.462 0.00 0.00 0.00 2.85
1393 1570 3.763057 GTACCCAACAACAAAGAGGGAT 58.237 45.455 2.29 0.00 42.25 3.85
1399 1576 2.289547 CACCTCGTACCCAACAACAAAG 59.710 50.000 0.00 0.00 0.00 2.77
1400 1577 2.290464 CACCTCGTACCCAACAACAAA 58.710 47.619 0.00 0.00 0.00 2.83
1401 1578 1.209990 ACACCTCGTACCCAACAACAA 59.790 47.619 0.00 0.00 0.00 2.83
1411 1588 1.605232 CCCCACAAAAACACCTCGTAC 59.395 52.381 0.00 0.00 0.00 3.67
1438 1615 1.281867 CCCAGCAGACACTCCCAATTA 59.718 52.381 0.00 0.00 0.00 1.40
1450 1627 0.966875 ATGCGCAAATTCCCAGCAGA 60.967 50.000 17.11 0.00 41.34 4.26
1454 1631 2.533266 GAGAAATGCGCAAATTCCCAG 58.467 47.619 26.33 0.00 0.00 4.45
1484 1661 4.621274 GCACTACCAATCAAACATGGCAAT 60.621 41.667 0.00 0.00 40.51 3.56
1490 1667 3.611530 GCAACGCACTACCAATCAAACAT 60.612 43.478 0.00 0.00 0.00 2.71
1516 1693 1.409427 GTATCCCGAAGTCTCCAGTGG 59.591 57.143 1.40 1.40 0.00 4.00
1531 1708 5.126061 AGCCAAACATGACAATCAAGTATCC 59.874 40.000 0.00 0.00 27.21 2.59
1565 1742 2.485426 ACACTGCAATCCAATTCAGTCG 59.515 45.455 0.00 0.00 37.66 4.18
1597 1774 8.739039 CCAAATCAGAAATCCAGTACAATTGTA 58.261 33.333 14.35 14.35 0.00 2.41
1598 1775 7.233348 ACCAAATCAGAAATCCAGTACAATTGT 59.767 33.333 16.68 16.68 0.00 2.71
1599 1776 7.605449 ACCAAATCAGAAATCCAGTACAATTG 58.395 34.615 3.24 3.24 0.00 2.32
1600 1777 7.781324 ACCAAATCAGAAATCCAGTACAATT 57.219 32.000 0.00 0.00 0.00 2.32
1601 1778 7.233348 ACAACCAAATCAGAAATCCAGTACAAT 59.767 33.333 0.00 0.00 0.00 2.71
1602 1779 6.549364 ACAACCAAATCAGAAATCCAGTACAA 59.451 34.615 0.00 0.00 0.00 2.41
1603 1780 6.068010 ACAACCAAATCAGAAATCCAGTACA 58.932 36.000 0.00 0.00 0.00 2.90
1604 1781 6.575162 ACAACCAAATCAGAAATCCAGTAC 57.425 37.500 0.00 0.00 0.00 2.73
1610 1787 9.994432 CATAGAGTAACAACCAAATCAGAAATC 57.006 33.333 0.00 0.00 0.00 2.17
1622 1799 3.181457 GGGGCTACCATAGAGTAACAACC 60.181 52.174 0.00 0.00 39.85 3.77
1636 1813 2.152016 GATAGCGAAAATGGGGCTACC 58.848 52.381 0.00 0.00 41.59 3.18
1660 1837 2.375174 AGAACCCAAGCTGTACCATCAA 59.625 45.455 0.00 0.00 0.00 2.57
1668 1845 1.898574 CCGCAAGAACCCAAGCTGT 60.899 57.895 0.00 0.00 43.02 4.40
1678 1855 6.653320 AGTCTTACATTCAAATACCGCAAGAA 59.347 34.615 0.00 0.00 43.02 2.52
1701 1878 4.631813 CGCTCTGCCATTTTCTAAACTAGT 59.368 41.667 0.00 0.00 0.00 2.57
1724 1901 0.109412 ATTGCAAAAGAGCTGAGCGC 60.109 50.000 1.71 0.00 39.57 5.92
1726 1903 2.415625 CCTCATTGCAAAAGAGCTGAGC 60.416 50.000 20.81 0.00 40.14 4.26
1727 1904 2.818432 ACCTCATTGCAAAAGAGCTGAG 59.182 45.455 20.81 18.22 40.14 3.35
1728 1905 2.867624 ACCTCATTGCAAAAGAGCTGA 58.132 42.857 20.81 11.18 40.14 4.26
1729 1906 4.771590 TTACCTCATTGCAAAAGAGCTG 57.228 40.909 20.81 13.54 40.14 4.24
1730 1907 5.717119 CATTTACCTCATTGCAAAAGAGCT 58.283 37.500 20.81 13.32 40.14 4.09
1731 1908 4.328169 GCATTTACCTCATTGCAAAAGAGC 59.672 41.667 20.81 9.52 40.14 4.09
1732 1909 4.866486 GGCATTTACCTCATTGCAAAAGAG 59.134 41.667 19.79 19.79 41.09 2.85
1733 1910 4.282957 TGGCATTTACCTCATTGCAAAAGA 59.717 37.500 1.71 3.82 36.82 2.52
1734 1911 4.567971 TGGCATTTACCTCATTGCAAAAG 58.432 39.130 1.71 4.08 36.82 2.27
1735 1912 4.613925 TGGCATTTACCTCATTGCAAAA 57.386 36.364 1.71 0.00 36.82 2.44
1736 1913 4.467082 AGATGGCATTTACCTCATTGCAAA 59.533 37.500 1.71 0.00 36.82 3.68
1737 1914 4.025360 AGATGGCATTTACCTCATTGCAA 58.975 39.130 0.00 0.00 36.82 4.08
1738 1915 3.382227 CAGATGGCATTTACCTCATTGCA 59.618 43.478 0.00 0.00 36.82 4.08
1757 1934 1.850345 ACCTCAAAAGACCCAACCAGA 59.150 47.619 0.00 0.00 0.00 3.86
1772 1949 3.474798 AGTATCACTTCTCCCACCTCA 57.525 47.619 0.00 0.00 0.00 3.86
1788 1965 1.522569 GCTGCCAGACCCGAAGTAT 59.477 57.895 0.00 0.00 0.00 2.12
1798 1975 2.999648 AGAGGAAGCGCTGCCAGA 61.000 61.111 35.98 0.00 0.00 3.86
1799 1976 2.818714 CAGAGGAAGCGCTGCCAG 60.819 66.667 35.98 21.02 0.00 4.85
1822 1999 2.159099 TCCACTGCGATGACTGGATAAC 60.159 50.000 0.00 0.00 0.00 1.89
1825 2002 0.904649 TTCCACTGCGATGACTGGAT 59.095 50.000 0.00 0.00 32.75 3.41
1828 2005 2.416747 TCTTTTCCACTGCGATGACTG 58.583 47.619 0.00 0.00 0.00 3.51
1847 2024 7.748847 TGTGAAACAGAAGTAGTCAGTTTTTC 58.251 34.615 0.00 0.00 45.67 2.29
1892 2069 8.253810 TGTAGTTCCTAGATCAACATTCTTCAG 58.746 37.037 0.00 0.00 0.00 3.02
1932 2109 4.407296 GGTATTCACAGGAGATTGGAGAGT 59.593 45.833 0.00 0.00 0.00 3.24
1940 2119 3.643792 GCCTACAGGTATTCACAGGAGAT 59.356 47.826 0.00 0.00 37.57 2.75
1955 2134 1.639635 ATTCTGGGGCCAGCCTACAG 61.640 60.000 20.62 20.62 43.31 2.74
2095 2274 3.008049 GGATGCACGGGAAGGATAATACT 59.992 47.826 0.00 0.00 0.00 2.12
2184 2363 4.908736 AGAATATTGTTCAAACGATGCCG 58.091 39.130 5.97 0.00 42.50 5.69
2233 2412 3.494223 CGGGAAAAGGAAGGCAAAATTGT 60.494 43.478 0.00 0.00 0.00 2.71
2247 2426 1.810755 GTAGGAAGGCAACGGGAAAAG 59.189 52.381 0.00 0.00 46.39 2.27
2263 2442 5.940192 TGTCAATAGCAGTTGTTTGTAGG 57.060 39.130 1.73 0.00 0.00 3.18
2268 2447 5.532406 AGTGTGATGTCAATAGCAGTTGTTT 59.468 36.000 1.73 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.