Multiple sequence alignment - TraesCS6D01G029300

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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 TraesCS6D01G029300 chr6D 100.000 3630 0 0 1 3630 11410617 11406988 0.000000e+00 6704
1 TraesCS6D01G029300 chr6D 84.518 394 58 3 3239 3630 11428561 11428953 1.580000e-103 387
2 TraesCS6D01G029300 chr6B 89.940 2326 110 60 672 2937 21286189 21283928 0.000000e+00 2885
3 TraesCS6D01G029300 chr6B 92.779 637 29 4 2995 3630 21278674 21278054 0.000000e+00 905
4 TraesCS6D01G029300 chr6B 89.105 514 49 5 180 691 21293460 21292952 1.840000e-177 632
5 TraesCS6D01G029300 chr6A 90.157 1717 106 27 312 2004 12838873 12837196 0.000000e+00 2176
6 TraesCS6D01G029300 chr6A 96.254 961 23 7 2047 2996 12837123 12836165 0.000000e+00 1563
7 TraesCS6D01G029300 chr6A 93.239 636 31 4 2996 3630 12836127 12835503 0.000000e+00 926
8 TraesCS6D01G029300 chr7D 81.148 488 84 7 228 710 509561123 509561607 5.690000e-103 385
9 TraesCS6D01G029300 chr3B 78.559 583 100 15 192 763 650809014 650808446 9.580000e-96 361
10 TraesCS6D01G029300 chr4D 78.230 565 111 12 201 757 484063111 484062551 5.770000e-93 351
11 TraesCS6D01G029300 chr2A 78.283 594 90 26 188 763 684440693 684440121 2.680000e-91 346
12 TraesCS6D01G029300 chr1B 77.817 568 118 7 192 755 312555331 312554768 9.650000e-91 344
13 TraesCS6D01G029300 chr3A 77.583 571 117 8 192 753 697287727 697287159 5.810000e-88 335
14 TraesCS6D01G029300 chr1D 77.487 573 111 13 192 755 218684233 218683670 9.720000e-86 327
15 TraesCS6D01G029300 chr1D 95.652 46 2 0 2106 2151 490324197 490324152 1.400000e-09 75
16 TraesCS6D01G029300 chr4B 77.562 566 107 16 201 755 15432216 15432772 1.260000e-84 324


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 TraesCS6D01G029300 chr6D 11406988 11410617 3629 True 6704 6704 100.000000 1 3630 1 chr6D.!!$R1 3629
1 TraesCS6D01G029300 chr6B 21283928 21286189 2261 True 2885 2885 89.940000 672 2937 1 chr6B.!!$R2 2265
2 TraesCS6D01G029300 chr6B 21278054 21278674 620 True 905 905 92.779000 2995 3630 1 chr6B.!!$R1 635
3 TraesCS6D01G029300 chr6B 21292952 21293460 508 True 632 632 89.105000 180 691 1 chr6B.!!$R3 511
4 TraesCS6D01G029300 chr6A 12835503 12838873 3370 True 1555 2176 93.216667 312 3630 3 chr6A.!!$R1 3318
5 TraesCS6D01G029300 chr3B 650808446 650809014 568 True 361 361 78.559000 192 763 1 chr3B.!!$R1 571
6 TraesCS6D01G029300 chr4D 484062551 484063111 560 True 351 351 78.230000 201 757 1 chr4D.!!$R1 556
7 TraesCS6D01G029300 chr2A 684440121 684440693 572 True 346 346 78.283000 188 763 1 chr2A.!!$R1 575
8 TraesCS6D01G029300 chr1B 312554768 312555331 563 True 344 344 77.817000 192 755 1 chr1B.!!$R1 563
9 TraesCS6D01G029300 chr3A 697287159 697287727 568 True 335 335 77.583000 192 753 1 chr3A.!!$R1 561
10 TraesCS6D01G029300 chr1D 218683670 218684233 563 True 327 327 77.487000 192 755 1 chr1D.!!$R1 563
11 TraesCS6D01G029300 chr4B 15432216 15432772 556 False 324 324 77.562000 201 755 1 chr4B.!!$F1 554

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
84 85 0.035915 GGGTGCCACCTCTTCTTCTC 60.036 60.0 14.71 0.0 38.64 2.87 F
1602 1679 0.542333 TGTTTCTTGACACGGGGACA 59.458 50.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1863 0.103937 GGTCGAGCAAGAGGAGATGG 59.896 60.0 10.3 0.00 0.0 3.51 R
2937 3117 0.028770 ACAACGCACGGACATGTTTG 59.971 50.0 0.0 0.84 0.0 2.93 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
18 19 3.050703 CGGGACCAACGAAGATGAG 57.949 57.895 0.00 0.00 29.10 2.90
19 20 0.530744 CGGGACCAACGAAGATGAGA 59.469 55.000 0.00 0.00 29.10 3.27
20 21 1.137086 CGGGACCAACGAAGATGAGAT 59.863 52.381 0.00 0.00 29.10 2.75
21 22 2.799917 CGGGACCAACGAAGATGAGATC 60.800 54.545 0.00 0.00 29.10 2.75
22 23 2.464865 GGACCAACGAAGATGAGATCG 58.535 52.381 0.00 0.00 44.33 3.69
23 24 2.464865 GACCAACGAAGATGAGATCGG 58.535 52.381 0.00 0.00 43.11 4.18
24 25 1.212616 CCAACGAAGATGAGATCGGC 58.787 55.000 0.00 0.00 43.11 5.54
25 26 1.212616 CAACGAAGATGAGATCGGCC 58.787 55.000 0.00 0.00 43.11 6.13
26 27 0.824109 AACGAAGATGAGATCGGCCA 59.176 50.000 2.24 0.00 43.11 5.36
27 28 0.103208 ACGAAGATGAGATCGGCCAC 59.897 55.000 2.24 0.00 43.11 5.01
28 29 0.598680 CGAAGATGAGATCGGCCACC 60.599 60.000 2.24 0.00 35.49 4.61
29 30 0.755686 GAAGATGAGATCGGCCACCT 59.244 55.000 2.24 0.00 0.00 4.00
30 31 0.755686 AAGATGAGATCGGCCACCTC 59.244 55.000 2.24 6.31 0.00 3.85
31 32 0.105760 AGATGAGATCGGCCACCTCT 60.106 55.000 2.24 0.05 0.00 3.69
32 33 0.755686 GATGAGATCGGCCACCTCTT 59.244 55.000 2.24 3.86 0.00 2.85
33 34 0.755686 ATGAGATCGGCCACCTCTTC 59.244 55.000 2.24 0.00 0.00 2.87
34 35 1.066587 GAGATCGGCCACCTCTTCG 59.933 63.158 2.24 0.00 0.00 3.79
35 36 1.379977 AGATCGGCCACCTCTTCGA 60.380 57.895 2.24 0.00 36.07 3.71
36 37 1.227002 GATCGGCCACCTCTTCGAC 60.227 63.158 2.24 0.00 34.40 4.20
37 38 1.945354 GATCGGCCACCTCTTCGACA 61.945 60.000 2.24 0.00 34.40 4.35
38 39 1.541310 ATCGGCCACCTCTTCGACAA 61.541 55.000 2.24 0.00 34.40 3.18
39 40 2.027625 CGGCCACCTCTTCGACAAC 61.028 63.158 2.24 0.00 0.00 3.32
40 41 1.671379 GGCCACCTCTTCGACAACC 60.671 63.158 0.00 0.00 0.00 3.77
41 42 1.371558 GCCACCTCTTCGACAACCT 59.628 57.895 0.00 0.00 0.00 3.50
42 43 0.250338 GCCACCTCTTCGACAACCTT 60.250 55.000 0.00 0.00 0.00 3.50
43 44 1.797025 CCACCTCTTCGACAACCTTC 58.203 55.000 0.00 0.00 0.00 3.46
44 45 1.608283 CCACCTCTTCGACAACCTTCC 60.608 57.143 0.00 0.00 0.00 3.46
45 46 0.317479 ACCTCTTCGACAACCTTCCG 59.683 55.000 0.00 0.00 0.00 4.30
46 47 1.014564 CCTCTTCGACAACCTTCCGC 61.015 60.000 0.00 0.00 0.00 5.54
47 48 1.005394 TCTTCGACAACCTTCCGCC 60.005 57.895 0.00 0.00 0.00 6.13
48 49 1.301401 CTTCGACAACCTTCCGCCA 60.301 57.895 0.00 0.00 0.00 5.69
49 50 1.566018 CTTCGACAACCTTCCGCCAC 61.566 60.000 0.00 0.00 0.00 5.01
50 51 2.280524 CGACAACCTTCCGCCACA 60.281 61.111 0.00 0.00 0.00 4.17
51 52 1.671054 CGACAACCTTCCGCCACAT 60.671 57.895 0.00 0.00 0.00 3.21
52 53 1.875963 GACAACCTTCCGCCACATG 59.124 57.895 0.00 0.00 0.00 3.21
53 54 0.605319 GACAACCTTCCGCCACATGA 60.605 55.000 0.00 0.00 0.00 3.07
54 55 0.179004 ACAACCTTCCGCCACATGAA 60.179 50.000 0.00 0.00 0.00 2.57
55 56 0.523072 CAACCTTCCGCCACATGAAG 59.477 55.000 0.00 0.00 38.14 3.02
56 57 0.400213 AACCTTCCGCCACATGAAGA 59.600 50.000 0.00 0.00 40.30 2.87
57 58 0.321653 ACCTTCCGCCACATGAAGAC 60.322 55.000 0.00 0.00 40.30 3.01
58 59 0.036010 CCTTCCGCCACATGAAGACT 60.036 55.000 0.00 0.00 40.30 3.24
59 60 1.207089 CCTTCCGCCACATGAAGACTA 59.793 52.381 0.00 0.00 40.30 2.59
60 61 2.271800 CTTCCGCCACATGAAGACTAC 58.728 52.381 0.00 0.00 40.30 2.73
61 62 0.172578 TCCGCCACATGAAGACTACG 59.827 55.000 0.00 0.00 0.00 3.51
62 63 0.108804 CCGCCACATGAAGACTACGT 60.109 55.000 0.00 0.00 0.00 3.57
63 64 1.269166 CGCCACATGAAGACTACGTC 58.731 55.000 0.00 0.00 0.00 4.34
64 65 1.269166 GCCACATGAAGACTACGTCG 58.731 55.000 0.00 0.00 37.67 5.12
65 66 1.909376 CCACATGAAGACTACGTCGG 58.091 55.000 0.00 0.00 37.67 4.79
66 67 1.469251 CCACATGAAGACTACGTCGGG 60.469 57.143 0.00 0.00 37.67 5.14
67 68 0.815734 ACATGAAGACTACGTCGGGG 59.184 55.000 0.00 0.00 37.67 5.73
68 69 0.815734 CATGAAGACTACGTCGGGGT 59.184 55.000 0.00 0.00 37.67 4.95
69 70 0.815734 ATGAAGACTACGTCGGGGTG 59.184 55.000 0.00 0.00 37.67 4.61
70 71 1.153881 GAAGACTACGTCGGGGTGC 60.154 63.158 0.00 0.00 37.67 5.01
71 72 2.554074 GAAGACTACGTCGGGGTGCC 62.554 65.000 0.00 0.00 37.67 5.01
72 73 3.376078 GACTACGTCGGGGTGCCA 61.376 66.667 0.00 0.00 0.00 4.92
73 74 3.637926 GACTACGTCGGGGTGCCAC 62.638 68.421 0.00 0.00 0.00 5.01
74 75 4.446413 CTACGTCGGGGTGCCACC 62.446 72.222 4.93 4.93 37.60 4.61
78 79 3.637273 GTCGGGGTGCCACCTCTT 61.637 66.667 12.90 0.00 36.29 2.85
79 80 3.319198 TCGGGGTGCCACCTCTTC 61.319 66.667 12.90 0.00 36.29 2.87
80 81 3.322466 CGGGGTGCCACCTCTTCT 61.322 66.667 12.90 0.00 36.29 2.85
81 82 2.895424 CGGGGTGCCACCTCTTCTT 61.895 63.158 12.90 0.00 36.29 2.52
82 83 1.002011 GGGGTGCCACCTCTTCTTC 60.002 63.158 14.71 0.00 35.29 2.87
83 84 1.492993 GGGGTGCCACCTCTTCTTCT 61.493 60.000 14.71 0.00 35.29 2.85
84 85 0.035915 GGGTGCCACCTCTTCTTCTC 60.036 60.000 14.71 0.00 38.64 2.87
85 86 0.980423 GGTGCCACCTCTTCTTCTCT 59.020 55.000 6.63 0.00 34.73 3.10
86 87 1.349357 GGTGCCACCTCTTCTTCTCTT 59.651 52.381 6.63 0.00 34.73 2.85
87 88 2.224646 GGTGCCACCTCTTCTTCTCTTT 60.225 50.000 6.63 0.00 34.73 2.52
88 89 3.481453 GTGCCACCTCTTCTTCTCTTTT 58.519 45.455 0.00 0.00 0.00 2.27
89 90 3.885901 GTGCCACCTCTTCTTCTCTTTTT 59.114 43.478 0.00 0.00 0.00 1.94
90 91 3.885297 TGCCACCTCTTCTTCTCTTTTTG 59.115 43.478 0.00 0.00 0.00 2.44
91 92 4.137543 GCCACCTCTTCTTCTCTTTTTGA 58.862 43.478 0.00 0.00 0.00 2.69
92 93 4.764308 GCCACCTCTTCTTCTCTTTTTGAT 59.236 41.667 0.00 0.00 0.00 2.57
93 94 5.335504 GCCACCTCTTCTTCTCTTTTTGATG 60.336 44.000 0.00 0.00 0.00 3.07
94 95 5.182760 CCACCTCTTCTTCTCTTTTTGATGG 59.817 44.000 0.00 0.00 0.00 3.51
95 96 5.767168 CACCTCTTCTTCTCTTTTTGATGGT 59.233 40.000 0.00 0.00 0.00 3.55
96 97 5.767168 ACCTCTTCTTCTCTTTTTGATGGTG 59.233 40.000 0.00 0.00 0.00 4.17
97 98 5.335504 CCTCTTCTTCTCTTTTTGATGGTGC 60.336 44.000 0.00 0.00 0.00 5.01
98 99 5.132502 TCTTCTTCTCTTTTTGATGGTGCA 58.867 37.500 0.00 0.00 0.00 4.57
99 100 5.593909 TCTTCTTCTCTTTTTGATGGTGCAA 59.406 36.000 0.00 0.00 0.00 4.08
100 101 6.266103 TCTTCTTCTCTTTTTGATGGTGCAAT 59.734 34.615 0.00 0.00 0.00 3.56
101 102 7.448161 TCTTCTTCTCTTTTTGATGGTGCAATA 59.552 33.333 0.00 0.00 0.00 1.90
102 103 7.707624 TCTTCTCTTTTTGATGGTGCAATAT 57.292 32.000 0.00 0.00 0.00 1.28
103 104 8.125978 TCTTCTCTTTTTGATGGTGCAATATT 57.874 30.769 0.00 0.00 0.00 1.28
104 105 8.030692 TCTTCTCTTTTTGATGGTGCAATATTG 58.969 33.333 11.27 11.27 0.00 1.90
105 106 7.230849 TCTCTTTTTGATGGTGCAATATTGT 57.769 32.000 16.61 0.00 0.00 2.71
106 107 7.092079 TCTCTTTTTGATGGTGCAATATTGTG 58.908 34.615 16.61 0.00 0.00 3.33
107 108 6.164876 TCTTTTTGATGGTGCAATATTGTGG 58.835 36.000 16.61 0.00 0.00 4.17
108 109 3.523606 TTGATGGTGCAATATTGTGGC 57.476 42.857 16.61 3.43 0.00 5.01
109 110 1.755959 TGATGGTGCAATATTGTGGCC 59.244 47.619 16.61 15.16 0.00 5.36
110 111 1.755959 GATGGTGCAATATTGTGGCCA 59.244 47.619 21.24 21.24 32.97 5.36
111 112 1.637338 TGGTGCAATATTGTGGCCAA 58.363 45.000 7.24 0.00 34.45 4.52
112 113 1.549620 TGGTGCAATATTGTGGCCAAG 59.450 47.619 7.24 0.00 33.17 3.61
113 114 1.643880 GTGCAATATTGTGGCCAAGC 58.356 50.000 7.24 3.81 33.17 4.01
126 127 3.012934 GGCCAAGCCCAACTATAAAGA 57.987 47.619 0.00 0.00 44.06 2.52
127 128 3.361786 GGCCAAGCCCAACTATAAAGAA 58.638 45.455 0.00 0.00 44.06 2.52
128 129 3.767131 GGCCAAGCCCAACTATAAAGAAA 59.233 43.478 0.00 0.00 44.06 2.52
129 130 4.221924 GGCCAAGCCCAACTATAAAGAAAA 59.778 41.667 0.00 0.00 44.06 2.29
130 131 5.168569 GCCAAGCCCAACTATAAAGAAAAC 58.831 41.667 0.00 0.00 0.00 2.43
131 132 5.720202 CCAAGCCCAACTATAAAGAAAACC 58.280 41.667 0.00 0.00 0.00 3.27
132 133 5.245075 CCAAGCCCAACTATAAAGAAAACCA 59.755 40.000 0.00 0.00 0.00 3.67
133 134 5.977489 AGCCCAACTATAAAGAAAACCAC 57.023 39.130 0.00 0.00 0.00 4.16
134 135 5.390387 AGCCCAACTATAAAGAAAACCACA 58.610 37.500 0.00 0.00 0.00 4.17
135 136 6.016555 AGCCCAACTATAAAGAAAACCACAT 58.983 36.000 0.00 0.00 0.00 3.21
136 137 6.071391 AGCCCAACTATAAAGAAAACCACATG 60.071 38.462 0.00 0.00 0.00 3.21
137 138 6.295067 GCCCAACTATAAAGAAAACCACATGT 60.295 38.462 0.00 0.00 0.00 3.21
138 139 7.312899 CCCAACTATAAAGAAAACCACATGTC 58.687 38.462 0.00 0.00 0.00 3.06
139 140 7.040062 CCCAACTATAAAGAAAACCACATGTCA 60.040 37.037 0.00 0.00 0.00 3.58
140 141 8.356657 CCAACTATAAAGAAAACCACATGTCAA 58.643 33.333 0.00 0.00 0.00 3.18
141 142 9.180678 CAACTATAAAGAAAACCACATGTCAAC 57.819 33.333 0.00 0.00 0.00 3.18
142 143 8.458573 ACTATAAAGAAAACCACATGTCAACA 57.541 30.769 0.00 0.00 0.00 3.33
143 144 9.077885 ACTATAAAGAAAACCACATGTCAACAT 57.922 29.630 0.00 0.00 36.96 2.71
146 147 6.959639 AAGAAAACCACATGTCAACATACT 57.040 33.333 0.00 0.00 34.26 2.12
147 148 6.317789 AGAAAACCACATGTCAACATACTG 57.682 37.500 0.00 0.00 34.26 2.74
148 149 4.503741 AAACCACATGTCAACATACTGC 57.496 40.909 0.00 0.00 34.26 4.40
149 150 3.138884 ACCACATGTCAACATACTGCA 57.861 42.857 0.00 0.00 34.26 4.41
150 151 3.485394 ACCACATGTCAACATACTGCAA 58.515 40.909 0.00 0.00 34.26 4.08
151 152 3.253188 ACCACATGTCAACATACTGCAAC 59.747 43.478 0.00 0.00 34.26 4.17
152 153 3.366273 CCACATGTCAACATACTGCAACC 60.366 47.826 0.00 0.00 34.26 3.77
153 154 3.252944 CACATGTCAACATACTGCAACCA 59.747 43.478 0.00 0.00 34.26 3.67
154 155 3.888323 ACATGTCAACATACTGCAACCAA 59.112 39.130 0.00 0.00 34.26 3.67
155 156 4.523943 ACATGTCAACATACTGCAACCAAT 59.476 37.500 0.00 0.00 34.26 3.16
156 157 4.502171 TGTCAACATACTGCAACCAATG 57.498 40.909 0.00 0.00 0.00 2.82
157 158 4.140536 TGTCAACATACTGCAACCAATGA 58.859 39.130 0.00 0.00 0.00 2.57
158 159 4.582240 TGTCAACATACTGCAACCAATGAA 59.418 37.500 0.00 0.00 0.00 2.57
159 160 5.156355 GTCAACATACTGCAACCAATGAAG 58.844 41.667 0.00 0.00 40.99 3.02
160 161 3.855689 ACATACTGCAACCAATGAAGC 57.144 42.857 0.00 0.00 38.40 3.86
161 162 3.156293 ACATACTGCAACCAATGAAGCA 58.844 40.909 0.00 0.00 38.40 3.91
162 163 3.573538 ACATACTGCAACCAATGAAGCAA 59.426 39.130 0.00 0.00 38.40 3.91
163 164 2.806608 ACTGCAACCAATGAAGCAAG 57.193 45.000 0.00 0.00 38.40 4.01
164 165 1.269936 ACTGCAACCAATGAAGCAAGC 60.270 47.619 0.00 0.00 38.40 4.01
165 166 0.751452 TGCAACCAATGAAGCAAGCA 59.249 45.000 0.00 0.00 33.48 3.91
166 167 1.138464 TGCAACCAATGAAGCAAGCAA 59.862 42.857 0.00 0.00 33.48 3.91
167 168 2.211806 GCAACCAATGAAGCAAGCAAA 58.788 42.857 0.00 0.00 0.00 3.68
168 169 2.613133 GCAACCAATGAAGCAAGCAAAA 59.387 40.909 0.00 0.00 0.00 2.44
169 170 3.303526 GCAACCAATGAAGCAAGCAAAAG 60.304 43.478 0.00 0.00 0.00 2.27
170 171 4.121317 CAACCAATGAAGCAAGCAAAAGA 58.879 39.130 0.00 0.00 0.00 2.52
171 172 3.986277 ACCAATGAAGCAAGCAAAAGAG 58.014 40.909 0.00 0.00 0.00 2.85
172 173 3.638160 ACCAATGAAGCAAGCAAAAGAGA 59.362 39.130 0.00 0.00 0.00 3.10
173 174 4.282703 ACCAATGAAGCAAGCAAAAGAGAT 59.717 37.500 0.00 0.00 0.00 2.75
174 175 4.625742 CCAATGAAGCAAGCAAAAGAGATG 59.374 41.667 0.00 0.00 0.00 2.90
175 176 5.466819 CAATGAAGCAAGCAAAAGAGATGA 58.533 37.500 0.00 0.00 0.00 2.92
176 177 5.916661 ATGAAGCAAGCAAAAGAGATGAT 57.083 34.783 0.00 0.00 0.00 2.45
177 178 5.055642 TGAAGCAAGCAAAAGAGATGATG 57.944 39.130 0.00 0.00 0.00 3.07
178 179 4.763279 TGAAGCAAGCAAAAGAGATGATGA 59.237 37.500 0.00 0.00 0.00 2.92
342 352 2.614057 CGGATAATGGCGCTTCTTCTTT 59.386 45.455 7.64 0.00 0.00 2.52
421 436 0.745468 AGTTCCGGCGTAGATTCCTC 59.255 55.000 6.01 0.00 0.00 3.71
463 478 3.000727 GGTTAGGGTTTCTCGTCATGTG 58.999 50.000 0.00 0.00 0.00 3.21
468 483 1.375396 TTTCTCGTCATGTGGGCGG 60.375 57.895 0.00 0.00 0.00 6.13
502 517 6.256757 GTCAGGTGTTTCAGATCTATACAAGC 59.743 42.308 0.00 0.00 0.00 4.01
540 560 2.409870 GGCTCCAGGGCATTGTTCG 61.410 63.158 0.00 0.00 40.53 3.95
598 619 1.880027 GACAAAGTCAACCGGCTCAAT 59.120 47.619 0.00 0.00 32.09 2.57
656 678 2.002586 CCGACAGCAATAGTGTCCTTG 58.997 52.381 0.00 0.00 41.17 3.61
682 707 6.433404 GGTGGTCTCGGAATCTCTATGTAATA 59.567 42.308 0.00 0.00 0.00 0.98
710 738 9.677567 TTATTTTGTTTGAGATGCTTTGTACTC 57.322 29.630 0.00 0.00 0.00 2.59
721 749 3.008157 TGCTTTGTACTCCCGGTGATTTA 59.992 43.478 0.00 0.00 0.00 1.40
730 758 8.484575 TGTACTCCCGGTGATTTATTACAATAA 58.515 33.333 0.00 0.00 0.00 1.40
795 835 3.568853 GGTTAGAGATGCGCTAAGGAGTA 59.431 47.826 9.73 0.00 0.00 2.59
804 844 2.924290 GCGCTAAGGAGTAGTTTCACAG 59.076 50.000 0.00 0.00 31.78 3.66
814 855 7.217906 AGGAGTAGTTTCACAGGTTAAGAAAG 58.782 38.462 0.00 0.00 32.48 2.62
828 869 9.877178 CAGGTTAAGAAAGAAATAGAGAAGCTA 57.123 33.333 0.00 0.00 0.00 3.32
854 900 2.362120 AGCACAAGAGGCCCATGC 60.362 61.111 0.00 2.21 36.52 4.06
987 1033 1.152139 CCCTCCTCTCATCCCCTCC 60.152 68.421 0.00 0.00 0.00 4.30
1423 1487 1.998315 CCTGCTCTGTTTCTGACGATG 59.002 52.381 0.00 0.00 0.00 3.84
1425 1489 1.338105 TGCTCTGTTTCTGACGATGGG 60.338 52.381 0.00 0.00 0.00 4.00
1525 1602 1.796749 GTCCTTCGACGTCGTGCTC 60.797 63.158 34.40 19.07 40.80 4.26
1564 1641 1.803922 CGACGCCGTCAAGTATGCA 60.804 57.895 18.40 0.00 32.09 3.96
1602 1679 0.542333 TGTTTCTTGACACGGGGACA 59.458 50.000 0.00 0.00 0.00 4.02
1630 1737 2.209273 AGGTTTGATTTTTGGTTGCGC 58.791 42.857 0.00 0.00 0.00 6.09
1755 1862 5.397360 GAGGGGGTAATCATTCATTCCATT 58.603 41.667 0.00 0.00 0.00 3.16
1756 1863 5.397360 AGGGGGTAATCATTCATTCCATTC 58.603 41.667 0.00 0.00 0.00 2.67
1758 1865 5.147032 GGGGTAATCATTCATTCCATTCCA 58.853 41.667 0.00 0.00 0.00 3.53
1761 1868 6.723052 GGGTAATCATTCATTCCATTCCATCT 59.277 38.462 0.00 0.00 0.00 2.90
1762 1869 7.094032 GGGTAATCATTCATTCCATTCCATCTC 60.094 40.741 0.00 0.00 0.00 2.75
1763 1870 6.912951 AATCATTCATTCCATTCCATCTCC 57.087 37.500 0.00 0.00 0.00 3.71
1764 1871 5.658198 TCATTCATTCCATTCCATCTCCT 57.342 39.130 0.00 0.00 0.00 3.69
1765 1872 5.628130 TCATTCATTCCATTCCATCTCCTC 58.372 41.667 0.00 0.00 0.00 3.71
1766 1873 5.371769 TCATTCATTCCATTCCATCTCCTCT 59.628 40.000 0.00 0.00 0.00 3.69
1767 1874 5.722172 TTCATTCCATTCCATCTCCTCTT 57.278 39.130 0.00 0.00 0.00 2.85
1768 1875 5.045012 TCATTCCATTCCATCTCCTCTTG 57.955 43.478 0.00 0.00 0.00 3.02
1769 1876 3.287867 TTCCATTCCATCTCCTCTTGC 57.712 47.619 0.00 0.00 0.00 4.01
1770 1877 2.485659 TCCATTCCATCTCCTCTTGCT 58.514 47.619 0.00 0.00 0.00 3.91
1774 1881 1.107114 TCCATCTCCTCTTGCTCGAC 58.893 55.000 0.00 0.00 0.00 4.20
1800 1907 1.140312 TCTTTGGTTGGTCAGAGGCT 58.860 50.000 0.00 0.00 0.00 4.58
1801 1908 1.072331 TCTTTGGTTGGTCAGAGGCTC 59.928 52.381 6.34 6.34 0.00 4.70
1802 1909 0.843309 TTTGGTTGGTCAGAGGCTCA 59.157 50.000 18.26 0.00 0.00 4.26
1803 1910 0.397941 TTGGTTGGTCAGAGGCTCAG 59.602 55.000 18.26 9.22 0.00 3.35
1804 1911 0.471780 TGGTTGGTCAGAGGCTCAGA 60.472 55.000 18.26 11.87 0.00 3.27
1805 1912 0.248843 GGTTGGTCAGAGGCTCAGAG 59.751 60.000 18.26 6.29 0.00 3.35
1806 1913 0.390998 GTTGGTCAGAGGCTCAGAGC 60.391 60.000 26.28 26.28 41.46 4.09
1823 1930 3.099524 GCTGAGTAGCCGATGATCG 57.900 57.895 8.05 8.05 44.33 3.69
1825 1932 1.535896 GCTGAGTAGCCGATGATCGTA 59.464 52.381 14.27 0.00 44.33 3.43
1827 1934 3.366476 GCTGAGTAGCCGATGATCGTAAT 60.366 47.826 14.27 0.00 44.33 1.89
1829 1936 4.795268 TGAGTAGCCGATGATCGTAATTC 58.205 43.478 14.27 5.65 38.40 2.17
1831 1938 3.572682 AGTAGCCGATGATCGTAATTCCA 59.427 43.478 14.27 0.00 38.40 3.53
1833 1940 3.589988 AGCCGATGATCGTAATTCCATC 58.410 45.455 14.27 0.00 38.40 3.51
1835 1942 4.462834 AGCCGATGATCGTAATTCCATCTA 59.537 41.667 14.27 0.00 38.40 1.98
1836 1943 4.563184 GCCGATGATCGTAATTCCATCTAC 59.437 45.833 14.27 0.00 38.40 2.59
1837 1944 4.793731 CCGATGATCGTAATTCCATCTACG 59.206 45.833 14.27 0.00 41.73 3.51
1838 1945 5.391449 CGATGATCGTAATTCCATCTACGT 58.609 41.667 6.68 0.00 41.26 3.57
1839 1946 5.856986 CGATGATCGTAATTCCATCTACGTT 59.143 40.000 6.68 0.00 41.26 3.99
1840 1947 6.183359 CGATGATCGTAATTCCATCTACGTTG 60.183 42.308 6.68 0.00 41.26 4.10
1841 1948 5.286438 TGATCGTAATTCCATCTACGTTGG 58.714 41.667 0.00 0.00 41.26 3.77
1904 2013 1.320344 TGGAGAAGTACATCGCGGCT 61.320 55.000 6.13 0.00 0.00 5.52
1995 2104 3.255149 GGAGTGGTTCTTCGACAGTAAGA 59.745 47.826 0.00 0.00 0.00 2.10
2039 2202 6.545504 TTACTTTCTGAGTTCTGACATTGC 57.454 37.500 0.00 0.00 39.86 3.56
2040 2203 4.454678 ACTTTCTGAGTTCTGACATTGCA 58.545 39.130 0.00 0.00 33.92 4.08
2041 2204 5.068636 ACTTTCTGAGTTCTGACATTGCAT 58.931 37.500 0.00 0.00 33.92 3.96
2042 2205 5.533903 ACTTTCTGAGTTCTGACATTGCATT 59.466 36.000 0.00 0.00 33.92 3.56
2043 2206 5.618056 TTCTGAGTTCTGACATTGCATTC 57.382 39.130 0.00 0.00 0.00 2.67
2044 2207 4.005650 TCTGAGTTCTGACATTGCATTCC 58.994 43.478 0.00 0.00 0.00 3.01
2045 2208 4.008330 CTGAGTTCTGACATTGCATTCCT 58.992 43.478 0.00 0.00 0.00 3.36
2046 2209 4.401022 TGAGTTCTGACATTGCATTCCTT 58.599 39.130 0.00 0.00 0.00 3.36
2047 2210 4.456911 TGAGTTCTGACATTGCATTCCTTC 59.543 41.667 0.00 0.00 0.00 3.46
2048 2211 4.660168 AGTTCTGACATTGCATTCCTTCT 58.340 39.130 0.00 0.00 0.00 2.85
2049 2212 5.075493 AGTTCTGACATTGCATTCCTTCTT 58.925 37.500 0.00 0.00 0.00 2.52
2050 2213 5.048224 AGTTCTGACATTGCATTCCTTCTTG 60.048 40.000 0.00 0.00 0.00 3.02
2051 2214 3.760151 TCTGACATTGCATTCCTTCTTGG 59.240 43.478 0.00 0.00 37.10 3.61
2052 2215 3.760151 CTGACATTGCATTCCTTCTTGGA 59.240 43.478 0.00 0.00 44.51 3.53
2053 2216 3.507233 TGACATTGCATTCCTTCTTGGAC 59.493 43.478 0.00 0.00 46.14 4.02
2392 2557 6.236967 CGATCGACATATAATTGTCACTACGC 60.237 42.308 10.26 0.00 45.08 4.42
2405 2570 2.278596 TACGCTCGCAATCTCCGC 60.279 61.111 0.00 0.00 0.00 5.54
2424 2593 3.106738 CATGGATTGGAGCCTGACC 57.893 57.895 0.00 0.00 0.00 4.02
2726 2899 5.462729 CAGATGACACAGAGCACATCTAATC 59.537 44.000 0.00 0.00 44.70 1.75
2766 2940 5.771602 TTTCTTTTTCTTTTGGAACGTGC 57.228 34.783 0.00 0.00 33.13 5.34
2873 3053 1.589803 AGGAAGGTTCAAACGAACGG 58.410 50.000 0.00 0.00 43.16 4.44
2946 3126 8.223769 CGATTATGTTAGGATAGCAAACATGTC 58.776 37.037 16.69 13.71 42.28 3.06
2956 3136 0.028770 CAAACATGTCCGTGCGTTGT 59.971 50.000 0.00 0.00 0.00 3.32
2967 3147 2.324860 CGTGCGTTGTAATGAGAGACA 58.675 47.619 0.00 0.00 0.00 3.41
3121 3340 2.999355 TGATTCAATGCATTCGACGTGA 59.001 40.909 9.53 0.00 0.00 4.35
3267 3486 2.231478 AGGTCACTACTCGTCCAATGTG 59.769 50.000 0.00 0.00 0.00 3.21
3293 3512 3.441101 TGTCTTACCTACTGCCATCACT 58.559 45.455 0.00 0.00 0.00 3.41
3298 3517 1.977854 ACCTACTGCCATCACTGTCAA 59.022 47.619 0.00 0.00 0.00 3.18
3319 3538 1.965754 GAGAGCCACTAGCCCACCAG 61.966 65.000 0.00 0.00 45.47 4.00
3391 3610 0.772124 TGCAGAACCCTTCCCCTTCT 60.772 55.000 0.00 0.00 0.00 2.85
3392 3611 0.405973 GCAGAACCCTTCCCCTTCTT 59.594 55.000 0.00 0.00 0.00 2.52
3393 3612 1.614583 GCAGAACCCTTCCCCTTCTTC 60.615 57.143 0.00 0.00 0.00 2.87
3394 3613 0.984995 AGAACCCTTCCCCTTCTTCG 59.015 55.000 0.00 0.00 0.00 3.79
3395 3614 0.677098 GAACCCTTCCCCTTCTTCGC 60.677 60.000 0.00 0.00 0.00 4.70
3396 3615 1.134438 AACCCTTCCCCTTCTTCGCT 61.134 55.000 0.00 0.00 0.00 4.93
3397 3616 1.134438 ACCCTTCCCCTTCTTCGCTT 61.134 55.000 0.00 0.00 0.00 4.68
3522 3741 2.780010 AGGGGATGAGGTGAATACAAGG 59.220 50.000 0.00 0.00 0.00 3.61
3524 3743 2.092429 GGGATGAGGTGAATACAAGGCA 60.092 50.000 0.00 0.00 0.00 4.75
3611 3830 2.017138 TCTCGTTGACACAAGCAACA 57.983 45.000 0.00 0.00 44.37 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.530744 TCTCATCTTCGTTGGTCCCG 59.469 55.000 0.00 0.00 0.00 5.14
1 2 2.799917 CGATCTCATCTTCGTTGGTCCC 60.800 54.545 0.00 0.00 0.00 4.46
2 3 2.464865 CGATCTCATCTTCGTTGGTCC 58.535 52.381 0.00 0.00 0.00 4.46
3 4 2.464865 CCGATCTCATCTTCGTTGGTC 58.535 52.381 0.00 0.00 33.60 4.02
4 5 1.471676 GCCGATCTCATCTTCGTTGGT 60.472 52.381 0.00 0.00 33.60 3.67
5 6 1.212616 GCCGATCTCATCTTCGTTGG 58.787 55.000 0.00 0.00 33.60 3.77
6 7 1.212616 GGCCGATCTCATCTTCGTTG 58.787 55.000 0.00 0.00 33.60 4.10
7 8 0.824109 TGGCCGATCTCATCTTCGTT 59.176 50.000 0.00 0.00 33.60 3.85
8 9 0.103208 GTGGCCGATCTCATCTTCGT 59.897 55.000 0.00 0.00 33.60 3.85
9 10 0.598680 GGTGGCCGATCTCATCTTCG 60.599 60.000 0.00 0.00 35.19 3.79
10 11 0.755686 AGGTGGCCGATCTCATCTTC 59.244 55.000 0.00 0.00 0.00 2.87
11 12 0.755686 GAGGTGGCCGATCTCATCTT 59.244 55.000 12.96 0.00 0.00 2.40
12 13 0.105760 AGAGGTGGCCGATCTCATCT 60.106 55.000 18.06 7.52 0.00 2.90
13 14 0.755686 AAGAGGTGGCCGATCTCATC 59.244 55.000 18.06 5.68 0.00 2.92
14 15 0.755686 GAAGAGGTGGCCGATCTCAT 59.244 55.000 18.06 9.20 0.00 2.90
15 16 1.667154 CGAAGAGGTGGCCGATCTCA 61.667 60.000 18.06 0.00 0.00 3.27
16 17 1.066587 CGAAGAGGTGGCCGATCTC 59.933 63.158 10.66 10.66 0.00 2.75
17 18 1.379977 TCGAAGAGGTGGCCGATCT 60.380 57.895 0.00 0.00 0.00 2.75
18 19 1.227002 GTCGAAGAGGTGGCCGATC 60.227 63.158 0.00 0.00 36.95 3.69
19 20 1.541310 TTGTCGAAGAGGTGGCCGAT 61.541 55.000 0.00 0.00 36.95 4.18
20 21 2.204461 TTGTCGAAGAGGTGGCCGA 61.204 57.895 0.00 0.00 36.95 5.54
21 22 2.027625 GTTGTCGAAGAGGTGGCCG 61.028 63.158 0.00 0.00 36.95 6.13
22 23 1.671379 GGTTGTCGAAGAGGTGGCC 60.671 63.158 0.00 0.00 36.95 5.36
23 24 0.250338 AAGGTTGTCGAAGAGGTGGC 60.250 55.000 0.00 0.00 36.95 5.01
24 25 1.608283 GGAAGGTTGTCGAAGAGGTGG 60.608 57.143 0.00 0.00 36.95 4.61
25 26 1.797025 GGAAGGTTGTCGAAGAGGTG 58.203 55.000 0.00 0.00 36.95 4.00
26 27 0.317479 CGGAAGGTTGTCGAAGAGGT 59.683 55.000 0.00 0.00 36.95 3.85
27 28 1.014564 GCGGAAGGTTGTCGAAGAGG 61.015 60.000 0.00 0.00 36.95 3.69
28 29 1.014564 GGCGGAAGGTTGTCGAAGAG 61.015 60.000 0.00 0.00 36.95 2.85
29 30 1.005394 GGCGGAAGGTTGTCGAAGA 60.005 57.895 0.00 0.00 0.00 2.87
30 31 1.301401 TGGCGGAAGGTTGTCGAAG 60.301 57.895 0.00 0.00 0.00 3.79
31 32 1.595929 GTGGCGGAAGGTTGTCGAA 60.596 57.895 0.00 0.00 0.00 3.71
32 33 2.029964 GTGGCGGAAGGTTGTCGA 59.970 61.111 0.00 0.00 0.00 4.20
33 34 1.671054 ATGTGGCGGAAGGTTGTCG 60.671 57.895 0.00 0.00 0.00 4.35
34 35 0.605319 TCATGTGGCGGAAGGTTGTC 60.605 55.000 0.00 0.00 0.00 3.18
35 36 0.179004 TTCATGTGGCGGAAGGTTGT 60.179 50.000 0.00 0.00 0.00 3.32
36 37 0.523072 CTTCATGTGGCGGAAGGTTG 59.477 55.000 0.00 0.00 37.46 3.77
37 38 0.400213 TCTTCATGTGGCGGAAGGTT 59.600 50.000 0.00 0.00 40.65 3.50
38 39 0.321653 GTCTTCATGTGGCGGAAGGT 60.322 55.000 0.00 0.00 40.65 3.50
39 40 0.036010 AGTCTTCATGTGGCGGAAGG 60.036 55.000 0.00 0.00 40.65 3.46
40 41 2.271800 GTAGTCTTCATGTGGCGGAAG 58.728 52.381 0.00 0.00 41.42 3.46
41 42 1.403647 CGTAGTCTTCATGTGGCGGAA 60.404 52.381 0.00 0.00 0.00 4.30
42 43 0.172578 CGTAGTCTTCATGTGGCGGA 59.827 55.000 0.00 0.00 0.00 5.54
43 44 0.108804 ACGTAGTCTTCATGTGGCGG 60.109 55.000 0.00 0.00 29.74 6.13
44 45 3.418675 ACGTAGTCTTCATGTGGCG 57.581 52.632 0.00 0.00 29.74 5.69
57 58 4.446413 GGTGGCACCCCGACGTAG 62.446 72.222 26.51 0.00 30.04 3.51
61 62 3.607370 GAAGAGGTGGCACCCCGAC 62.607 68.421 32.30 20.28 39.75 4.79
62 63 3.319198 GAAGAGGTGGCACCCCGA 61.319 66.667 32.30 0.00 39.75 5.14
63 64 2.804828 GAAGAAGAGGTGGCACCCCG 62.805 65.000 32.30 0.00 39.75 5.73
64 65 1.002011 GAAGAAGAGGTGGCACCCC 60.002 63.158 32.30 22.46 39.75 4.95
65 66 0.035915 GAGAAGAAGAGGTGGCACCC 60.036 60.000 32.30 22.79 39.75 4.61
66 67 0.980423 AGAGAAGAAGAGGTGGCACC 59.020 55.000 29.32 29.32 38.99 5.01
67 68 2.849294 AAGAGAAGAAGAGGTGGCAC 57.151 50.000 9.70 9.70 0.00 5.01
68 69 3.864789 AAAAGAGAAGAAGAGGTGGCA 57.135 42.857 0.00 0.00 0.00 4.92
69 70 4.137543 TCAAAAAGAGAAGAAGAGGTGGC 58.862 43.478 0.00 0.00 0.00 5.01
70 71 5.182760 CCATCAAAAAGAGAAGAAGAGGTGG 59.817 44.000 0.00 0.00 0.00 4.61
71 72 5.767168 ACCATCAAAAAGAGAAGAAGAGGTG 59.233 40.000 0.00 0.00 0.00 4.00
72 73 5.767168 CACCATCAAAAAGAGAAGAAGAGGT 59.233 40.000 0.00 0.00 0.00 3.85
73 74 5.335504 GCACCATCAAAAAGAGAAGAAGAGG 60.336 44.000 0.00 0.00 0.00 3.69
74 75 5.240183 TGCACCATCAAAAAGAGAAGAAGAG 59.760 40.000 0.00 0.00 0.00 2.85
75 76 5.132502 TGCACCATCAAAAAGAGAAGAAGA 58.867 37.500 0.00 0.00 0.00 2.87
76 77 5.443185 TGCACCATCAAAAAGAGAAGAAG 57.557 39.130 0.00 0.00 0.00 2.85
77 78 5.850557 TTGCACCATCAAAAAGAGAAGAA 57.149 34.783 0.00 0.00 0.00 2.52
78 79 7.707624 ATATTGCACCATCAAAAAGAGAAGA 57.292 32.000 0.00 0.00 0.00 2.87
79 80 7.816031 ACAATATTGCACCATCAAAAAGAGAAG 59.184 33.333 15.48 0.00 0.00 2.85
80 81 7.599621 CACAATATTGCACCATCAAAAAGAGAA 59.400 33.333 15.48 0.00 0.00 2.87
81 82 7.092079 CACAATATTGCACCATCAAAAAGAGA 58.908 34.615 15.48 0.00 0.00 3.10
82 83 6.311935 CCACAATATTGCACCATCAAAAAGAG 59.688 38.462 15.48 0.00 0.00 2.85
83 84 6.164876 CCACAATATTGCACCATCAAAAAGA 58.835 36.000 15.48 0.00 0.00 2.52
84 85 5.163834 GCCACAATATTGCACCATCAAAAAG 60.164 40.000 15.48 0.00 0.00 2.27
85 86 4.694509 GCCACAATATTGCACCATCAAAAA 59.305 37.500 15.48 0.00 0.00 1.94
86 87 4.252073 GCCACAATATTGCACCATCAAAA 58.748 39.130 15.48 0.00 0.00 2.44
87 88 3.369261 GGCCACAATATTGCACCATCAAA 60.369 43.478 15.48 0.00 0.00 2.69
88 89 2.168106 GGCCACAATATTGCACCATCAA 59.832 45.455 15.48 0.00 0.00 2.57
89 90 1.755959 GGCCACAATATTGCACCATCA 59.244 47.619 15.48 0.00 0.00 3.07
90 91 1.755959 TGGCCACAATATTGCACCATC 59.244 47.619 15.48 1.95 0.00 3.51
91 92 1.863325 TGGCCACAATATTGCACCAT 58.137 45.000 15.48 0.00 0.00 3.55
92 93 1.549620 CTTGGCCACAATATTGCACCA 59.450 47.619 15.48 16.14 35.73 4.17
93 94 1.740043 GCTTGGCCACAATATTGCACC 60.740 52.381 15.48 13.89 35.73 5.01
94 95 1.643880 GCTTGGCCACAATATTGCAC 58.356 50.000 15.48 5.01 35.73 4.57
107 108 5.168569 GTTTTCTTTATAGTTGGGCTTGGC 58.831 41.667 0.00 0.00 0.00 4.52
108 109 5.245075 TGGTTTTCTTTATAGTTGGGCTTGG 59.755 40.000 0.00 0.00 0.00 3.61
109 110 6.156519 GTGGTTTTCTTTATAGTTGGGCTTG 58.843 40.000 0.00 0.00 0.00 4.01
110 111 5.836358 TGTGGTTTTCTTTATAGTTGGGCTT 59.164 36.000 0.00 0.00 0.00 4.35
111 112 5.390387 TGTGGTTTTCTTTATAGTTGGGCT 58.610 37.500 0.00 0.00 0.00 5.19
112 113 5.715434 TGTGGTTTTCTTTATAGTTGGGC 57.285 39.130 0.00 0.00 0.00 5.36
113 114 7.040062 TGACATGTGGTTTTCTTTATAGTTGGG 60.040 37.037 1.15 0.00 0.00 4.12
114 115 7.881142 TGACATGTGGTTTTCTTTATAGTTGG 58.119 34.615 1.15 0.00 0.00 3.77
115 116 9.180678 GTTGACATGTGGTTTTCTTTATAGTTG 57.819 33.333 1.15 0.00 0.00 3.16
116 117 8.908903 TGTTGACATGTGGTTTTCTTTATAGTT 58.091 29.630 1.15 0.00 0.00 2.24
117 118 8.458573 TGTTGACATGTGGTTTTCTTTATAGT 57.541 30.769 1.15 0.00 0.00 2.12
120 121 9.077885 AGTATGTTGACATGTGGTTTTCTTTAT 57.922 29.630 1.15 0.00 37.15 1.40
121 122 8.349245 CAGTATGTTGACATGTGGTTTTCTTTA 58.651 33.333 1.15 0.00 37.15 1.85
122 123 7.202526 CAGTATGTTGACATGTGGTTTTCTTT 58.797 34.615 1.15 0.00 37.15 2.52
123 124 6.735694 GCAGTATGTTGACATGTGGTTTTCTT 60.736 38.462 1.15 0.00 39.31 2.52
124 125 5.278463 GCAGTATGTTGACATGTGGTTTTCT 60.278 40.000 1.15 0.00 39.31 2.52
125 126 4.917415 GCAGTATGTTGACATGTGGTTTTC 59.083 41.667 1.15 0.00 39.31 2.29
126 127 4.340666 TGCAGTATGTTGACATGTGGTTTT 59.659 37.500 1.15 0.00 39.31 2.43
127 128 3.888323 TGCAGTATGTTGACATGTGGTTT 59.112 39.130 1.15 0.00 39.31 3.27
128 129 3.485394 TGCAGTATGTTGACATGTGGTT 58.515 40.909 1.15 0.00 39.31 3.67
129 130 3.138884 TGCAGTATGTTGACATGTGGT 57.861 42.857 1.15 0.00 39.31 4.16
130 131 3.366273 GGTTGCAGTATGTTGACATGTGG 60.366 47.826 1.15 0.00 39.31 4.17
131 132 3.252944 TGGTTGCAGTATGTTGACATGTG 59.747 43.478 1.15 5.62 39.31 3.21
132 133 3.485394 TGGTTGCAGTATGTTGACATGT 58.515 40.909 0.00 0.00 39.31 3.21
133 134 4.502171 TTGGTTGCAGTATGTTGACATG 57.498 40.909 6.87 0.00 39.31 3.21
134 135 4.766373 TCATTGGTTGCAGTATGTTGACAT 59.234 37.500 1.84 1.84 39.31 3.06
135 136 4.140536 TCATTGGTTGCAGTATGTTGACA 58.859 39.130 0.00 0.00 39.31 3.58
136 137 4.764679 TCATTGGTTGCAGTATGTTGAC 57.235 40.909 0.00 0.00 39.31 3.18
137 138 4.321156 GCTTCATTGGTTGCAGTATGTTGA 60.321 41.667 0.00 0.00 39.31 3.18
138 139 3.922240 GCTTCATTGGTTGCAGTATGTTG 59.078 43.478 0.00 0.00 39.31 3.33
139 140 3.573538 TGCTTCATTGGTTGCAGTATGTT 59.426 39.130 0.00 0.00 39.31 2.71
140 141 3.156293 TGCTTCATTGGTTGCAGTATGT 58.844 40.909 0.00 0.00 39.31 2.29
141 142 3.853831 TGCTTCATTGGTTGCAGTATG 57.146 42.857 0.00 0.00 40.87 2.39
142 143 3.367703 GCTTGCTTCATTGGTTGCAGTAT 60.368 43.478 0.00 0.00 36.75 2.12
143 144 2.030007 GCTTGCTTCATTGGTTGCAGTA 60.030 45.455 0.00 0.00 36.75 2.74
144 145 1.269936 GCTTGCTTCATTGGTTGCAGT 60.270 47.619 0.00 0.00 36.75 4.40
145 146 1.269883 TGCTTGCTTCATTGGTTGCAG 60.270 47.619 0.00 0.00 36.75 4.41
146 147 0.751452 TGCTTGCTTCATTGGTTGCA 59.249 45.000 0.00 0.00 0.00 4.08
147 148 1.868469 TTGCTTGCTTCATTGGTTGC 58.132 45.000 0.00 0.00 0.00 4.17
148 149 4.121317 TCTTTTGCTTGCTTCATTGGTTG 58.879 39.130 0.00 0.00 0.00 3.77
149 150 4.099881 TCTCTTTTGCTTGCTTCATTGGTT 59.900 37.500 0.00 0.00 0.00 3.67
150 151 3.638160 TCTCTTTTGCTTGCTTCATTGGT 59.362 39.130 0.00 0.00 0.00 3.67
151 152 4.247267 TCTCTTTTGCTTGCTTCATTGG 57.753 40.909 0.00 0.00 0.00 3.16
152 153 5.466819 TCATCTCTTTTGCTTGCTTCATTG 58.533 37.500 0.00 0.00 0.00 2.82
153 154 5.717078 TCATCTCTTTTGCTTGCTTCATT 57.283 34.783 0.00 0.00 0.00 2.57
154 155 5.417894 TCATCATCTCTTTTGCTTGCTTCAT 59.582 36.000 0.00 0.00 0.00 2.57
155 156 4.763279 TCATCATCTCTTTTGCTTGCTTCA 59.237 37.500 0.00 0.00 0.00 3.02
156 157 5.306532 TCATCATCTCTTTTGCTTGCTTC 57.693 39.130 0.00 0.00 0.00 3.86
157 158 5.417894 TGATCATCATCTCTTTTGCTTGCTT 59.582 36.000 0.00 0.00 0.00 3.91
158 159 4.948004 TGATCATCATCTCTTTTGCTTGCT 59.052 37.500 0.00 0.00 0.00 3.91
159 160 5.244785 TGATCATCATCTCTTTTGCTTGC 57.755 39.130 0.00 0.00 0.00 4.01
160 161 7.480810 TCATTGATCATCATCTCTTTTGCTTG 58.519 34.615 0.00 0.00 0.00 4.01
161 162 7.640597 TCATTGATCATCATCTCTTTTGCTT 57.359 32.000 0.00 0.00 0.00 3.91
162 163 7.640597 TTCATTGATCATCATCTCTTTTGCT 57.359 32.000 0.00 0.00 0.00 3.91
163 164 6.418226 GCTTCATTGATCATCATCTCTTTTGC 59.582 38.462 0.00 0.00 0.00 3.68
164 165 6.918569 GGCTTCATTGATCATCATCTCTTTTG 59.081 38.462 0.00 0.00 0.00 2.44
165 166 6.605995 TGGCTTCATTGATCATCATCTCTTTT 59.394 34.615 0.00 0.00 0.00 2.27
166 167 6.127101 TGGCTTCATTGATCATCATCTCTTT 58.873 36.000 0.00 0.00 0.00 2.52
167 168 5.691896 TGGCTTCATTGATCATCATCTCTT 58.308 37.500 0.00 0.00 0.00 2.85
168 169 5.306114 TGGCTTCATTGATCATCATCTCT 57.694 39.130 0.00 0.00 0.00 3.10
169 170 5.563085 GCTTGGCTTCATTGATCATCATCTC 60.563 44.000 0.00 0.00 0.00 2.75
170 171 4.278669 GCTTGGCTTCATTGATCATCATCT 59.721 41.667 0.00 0.00 0.00 2.90
171 172 4.547532 GCTTGGCTTCATTGATCATCATC 58.452 43.478 0.00 0.00 0.00 2.92
172 173 3.321111 GGCTTGGCTTCATTGATCATCAT 59.679 43.478 0.00 0.00 0.00 2.45
173 174 2.691526 GGCTTGGCTTCATTGATCATCA 59.308 45.455 0.00 0.00 0.00 3.07
174 175 2.035576 GGGCTTGGCTTCATTGATCATC 59.964 50.000 0.00 0.00 0.00 2.92
175 176 2.037144 GGGCTTGGCTTCATTGATCAT 58.963 47.619 0.00 0.00 0.00 2.45
176 177 1.477553 GGGCTTGGCTTCATTGATCA 58.522 50.000 0.00 0.00 0.00 2.92
177 178 0.383231 CGGGCTTGGCTTCATTGATC 59.617 55.000 0.00 0.00 0.00 2.92
178 179 0.323725 ACGGGCTTGGCTTCATTGAT 60.324 50.000 0.00 0.00 0.00 2.57
254 259 1.347707 CTAACCAGAACAGAGGCACCA 59.652 52.381 0.00 0.00 0.00 4.17
421 436 2.810486 GTCGTCCCAAGAAGACACG 58.190 57.895 4.58 0.00 46.87 4.49
463 478 2.034999 TGACACCAAATCCCGCCC 59.965 61.111 0.00 0.00 0.00 6.13
468 483 2.955660 TGAAACACCTGACACCAAATCC 59.044 45.455 0.00 0.00 0.00 3.01
502 517 1.119497 CGTAGTTGTCGTCGTTGAACG 59.881 52.381 12.12 12.12 44.19 3.95
540 560 3.419759 CGTGCACGTGCCCCTAAC 61.420 66.667 35.72 25.06 41.18 2.34
558 578 2.034685 TCGATGATAGCCGGAAAGTCTG 59.965 50.000 5.05 0.00 0.00 3.51
637 658 2.002586 CCAAGGACACTATTGCTGTCG 58.997 52.381 0.00 0.00 39.23 4.35
656 678 2.068834 TAGAGATTCCGAGACCACCC 57.931 55.000 0.00 0.00 0.00 4.61
689 717 4.518970 GGGAGTACAAAGCATCTCAAACAA 59.481 41.667 0.00 0.00 0.00 2.83
795 835 9.847224 TCTATTTCTTTCTTAACCTGTGAAACT 57.153 29.630 0.00 0.00 38.04 2.66
804 844 9.320352 CCTAGCTTCTCTATTTCTTTCTTAACC 57.680 37.037 0.00 0.00 0.00 2.85
814 855 4.406003 TGGTCCACCTAGCTTCTCTATTTC 59.594 45.833 0.00 0.00 36.82 2.17
828 869 1.757306 CTCTTGTGCTGGTCCACCT 59.243 57.895 0.00 0.00 34.85 4.00
829 870 1.302832 CCTCTTGTGCTGGTCCACC 60.303 63.158 0.00 0.00 34.85 4.61
854 900 1.218316 GTCGTTGGTGGCCTAGAGG 59.782 63.158 3.32 0.00 38.53 3.69
865 911 1.231221 TGAATTTGTCGGGTCGTTGG 58.769 50.000 0.00 0.00 0.00 3.77
966 1012 1.841103 GGGGATGAGAGGAGGGAGC 60.841 68.421 0.00 0.00 0.00 4.70
987 1033 2.801631 GGCCATGGAGGAGGACGAG 61.802 68.421 18.40 0.00 41.22 4.18
1375 1424 1.068474 CCGATCACAAACTCCGACAC 58.932 55.000 0.00 0.00 0.00 3.67
1376 1425 0.963225 TCCGATCACAAACTCCGACA 59.037 50.000 0.00 0.00 0.00 4.35
1423 1487 1.673665 CAGCTCCTGCACAGAACCC 60.674 63.158 0.00 0.00 42.74 4.11
1425 1489 1.287730 CGTCAGCTCCTGCACAGAAC 61.288 60.000 0.00 0.00 42.74 3.01
1525 1602 0.317519 GGTCCTTGCCGTTGTTTTCG 60.318 55.000 0.00 0.00 0.00 3.46
1602 1679 3.004734 CCAAAAATCAAACCTCACGCTCT 59.995 43.478 0.00 0.00 0.00 4.09
1755 1862 1.107114 GTCGAGCAAGAGGAGATGGA 58.893 55.000 0.00 0.00 0.00 3.41
1756 1863 0.103937 GGTCGAGCAAGAGGAGATGG 59.896 60.000 10.30 0.00 0.00 3.51
1758 1865 1.561643 TTGGTCGAGCAAGAGGAGAT 58.438 50.000 25.16 0.00 0.00 2.75
1761 1868 0.976641 ACATTGGTCGAGCAAGAGGA 59.023 50.000 30.90 12.00 0.00 3.71
1762 1869 1.734465 GAACATTGGTCGAGCAAGAGG 59.266 52.381 30.90 24.24 0.00 3.69
1763 1870 2.693069 AGAACATTGGTCGAGCAAGAG 58.307 47.619 30.90 26.57 0.00 2.85
1764 1871 2.839486 AGAACATTGGTCGAGCAAGA 57.161 45.000 30.90 13.48 0.00 3.02
1765 1872 3.558505 CAAAGAACATTGGTCGAGCAAG 58.441 45.455 30.90 24.11 0.00 4.01
1766 1873 2.293122 CCAAAGAACATTGGTCGAGCAA 59.707 45.455 30.00 30.00 43.99 3.91
1767 1874 1.879380 CCAAAGAACATTGGTCGAGCA 59.121 47.619 14.39 14.39 43.99 4.26
1768 1875 2.619013 CCAAAGAACATTGGTCGAGC 57.381 50.000 7.89 7.89 43.99 5.03
1805 1912 0.312416 ACGATCATCGGCTACTCAGC 59.688 55.000 12.67 0.00 45.59 4.26
1806 1913 3.898517 TTACGATCATCGGCTACTCAG 57.101 47.619 12.67 0.00 45.59 3.35
1831 1938 0.458543 CTGCGAGCACCAACGTAGAT 60.459 55.000 0.00 0.00 42.77 1.98
1833 1940 2.094659 CCTGCGAGCACCAACGTAG 61.095 63.158 0.00 0.00 40.65 3.51
1835 1942 3.923864 TCCTGCGAGCACCAACGT 61.924 61.111 0.00 0.00 0.00 3.99
1836 1943 3.414700 GTCCTGCGAGCACCAACG 61.415 66.667 0.00 0.00 0.00 4.10
1837 1944 3.414700 CGTCCTGCGAGCACCAAC 61.415 66.667 0.00 0.00 44.77 3.77
1877 1986 1.116536 TGTACTTCTCCACGCCCACA 61.117 55.000 0.00 0.00 0.00 4.17
1880 1989 0.527817 CGATGTACTTCTCCACGCCC 60.528 60.000 7.13 0.00 0.00 6.13
1904 2013 4.704833 GCCCAGCTGCCGAACTCA 62.705 66.667 8.66 0.00 0.00 3.41
2018 2181 4.454678 TGCAATGTCAGAACTCAGAAAGT 58.545 39.130 0.00 0.00 41.10 2.66
2020 2183 5.048504 GGAATGCAATGTCAGAACTCAGAAA 60.049 40.000 0.00 0.00 0.00 2.52
2025 2188 4.699257 AGAAGGAATGCAATGTCAGAACTC 59.301 41.667 0.00 0.00 0.00 3.01
2026 2189 4.660168 AGAAGGAATGCAATGTCAGAACT 58.340 39.130 0.00 0.00 0.00 3.01
2028 2191 4.219070 CCAAGAAGGAATGCAATGTCAGAA 59.781 41.667 0.00 0.00 41.22 3.02
2030 2193 3.760151 TCCAAGAAGGAATGCAATGTCAG 59.240 43.478 0.00 0.00 45.65 3.51
2031 2194 3.765381 TCCAAGAAGGAATGCAATGTCA 58.235 40.909 0.00 0.00 45.65 3.58
2042 2205 6.306199 TCATTTCATTTCAGTCCAAGAAGGA 58.694 36.000 0.00 0.00 46.75 3.36
2043 2206 6.579666 TCATTTCATTTCAGTCCAAGAAGG 57.420 37.500 0.00 0.00 39.47 3.46
2044 2207 8.922676 CATTTCATTTCATTTCAGTCCAAGAAG 58.077 33.333 0.00 0.00 0.00 2.85
2045 2208 7.874016 CCATTTCATTTCATTTCAGTCCAAGAA 59.126 33.333 0.00 0.00 0.00 2.52
2046 2209 7.380536 CCATTTCATTTCATTTCAGTCCAAGA 58.619 34.615 0.00 0.00 0.00 3.02
2047 2210 6.592607 CCCATTTCATTTCATTTCAGTCCAAG 59.407 38.462 0.00 0.00 0.00 3.61
2048 2211 6.465948 CCCATTTCATTTCATTTCAGTCCAA 58.534 36.000 0.00 0.00 0.00 3.53
2049 2212 5.569227 GCCCATTTCATTTCATTTCAGTCCA 60.569 40.000 0.00 0.00 0.00 4.02
2050 2213 4.872124 GCCCATTTCATTTCATTTCAGTCC 59.128 41.667 0.00 0.00 0.00 3.85
2051 2214 5.481105 TGCCCATTTCATTTCATTTCAGTC 58.519 37.500 0.00 0.00 0.00 3.51
2052 2215 5.484715 CTGCCCATTTCATTTCATTTCAGT 58.515 37.500 0.00 0.00 0.00 3.41
2053 2216 4.873827 CCTGCCCATTTCATTTCATTTCAG 59.126 41.667 0.00 0.00 0.00 3.02
2392 2557 2.249535 CCATGGCGGAGATTGCGAG 61.250 63.158 0.00 0.00 36.56 5.03
2424 2593 3.587797 AGAAATGCTGCAACCATCTTG 57.412 42.857 6.36 0.00 0.00 3.02
2758 2932 2.125512 ATCAGGCTCGCACGTTCC 60.126 61.111 0.00 0.00 0.00 3.62
2766 2940 0.179089 AGCTACTTGCATCAGGCTCG 60.179 55.000 0.00 0.00 45.94 5.03
2879 3059 5.011533 GTGTGATTGCCTATATCTCCTCTGT 59.988 44.000 0.00 0.00 0.00 3.41
2937 3117 0.028770 ACAACGCACGGACATGTTTG 59.971 50.000 0.00 0.84 0.00 2.93
2946 3126 1.654105 GTCTCTCATTACAACGCACGG 59.346 52.381 0.00 0.00 0.00 4.94
2983 3163 3.314553 CGACCGTGTTACTCATTTGACT 58.685 45.455 0.00 0.00 0.00 3.41
2984 3164 2.159881 GCGACCGTGTTACTCATTTGAC 60.160 50.000 0.00 0.00 0.00 3.18
3029 3247 1.282248 CGTGATCAGCGACCGTGTTT 61.282 55.000 10.86 0.00 0.00 2.83
3030 3248 1.733041 CGTGATCAGCGACCGTGTT 60.733 57.895 10.86 0.00 0.00 3.32
3031 3249 2.126463 CGTGATCAGCGACCGTGT 60.126 61.111 10.86 0.00 0.00 4.49
3121 3340 5.163374 GCAAGCTCATTCCTTTGGGATTTAT 60.163 40.000 0.00 0.00 41.87 1.40
3163 3382 3.582120 CTTGCACGGCACAACGGT 61.582 61.111 0.00 0.00 38.71 4.83
3164 3383 4.326766 CCTTGCACGGCACAACGG 62.327 66.667 0.00 0.00 38.71 4.44
3166 3385 1.805428 ATTCCCTTGCACGGCACAAC 61.805 55.000 3.07 0.00 38.71 3.32
3248 3467 2.607187 CCACATTGGACGAGTAGTGAC 58.393 52.381 0.00 0.00 40.96 3.67
3267 3486 1.065636 GGCAGTAGGTAAGACAACCCC 60.066 57.143 0.00 0.00 40.71 4.95
3293 3512 0.898320 GCTAGTGGCTCTCCTTGACA 59.102 55.000 0.00 0.00 38.06 3.58
3298 3517 1.687493 GTGGGCTAGTGGCTCTCCT 60.687 63.158 0.00 0.00 43.07 3.69
3350 3569 3.677156 AATGAGAAGGAAGAATGGGGG 57.323 47.619 0.00 0.00 0.00 5.40
3471 3690 5.435291 CCCTTGTATTTTCTCATCTCTGCT 58.565 41.667 0.00 0.00 0.00 4.24
3522 3741 5.462068 GGTGTTTCTTTATTTTCTGGTGTGC 59.538 40.000 0.00 0.00 0.00 4.57
3524 3743 6.783708 TGGTGTTTCTTTATTTTCTGGTGT 57.216 33.333 0.00 0.00 0.00 4.16
3575 3794 4.554292 ACGAGATATGACATAGCAAGCAG 58.446 43.478 12.95 2.40 0.00 4.24
3611 3830 1.308326 AGCTAGAGCCCTTCTCCGT 59.692 57.895 0.00 0.00 42.90 4.69


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

AutoCloner maintained by Alex Coulton.