Multiple sequence alignment - TraesCS1D01G254800

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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 TraesCS1D01G254800 chr1D 100.000 5221 0 0 1 5221 347220364 347215144 0.000000e+00 9642.0
1 TraesCS1D01G254800 chr1B 94.387 4240 140 39 642 4843 467934456 467930277 0.000000e+00 6421.0
2 TraesCS1D01G254800 chr1B 85.407 418 32 17 182 578 467934992 467934583 1.750000e-109 407.0
3 TraesCS1D01G254800 chr1B 92.638 163 9 2 5058 5219 467926954 467926794 1.130000e-56 231.0
4 TraesCS1D01G254800 chr1B 94.531 128 5 2 4849 4975 467927096 467926970 4.120000e-46 196.0
5 TraesCS1D01G254800 chr1B 88.462 52 2 2 595 642 467934538 467934487 5.650000e-05 60.2
6 TraesCS1D01G254800 chr1A 91.430 2392 87 50 276 2601 447644891 447642552 0.000000e+00 3173.0
7 TraesCS1D01G254800 chr1A 96.934 1598 43 5 2718 4309 447642509 447640912 0.000000e+00 2675.0
8 TraesCS1D01G254800 chr1A 92.287 739 39 7 4251 4975 447640918 447640184 0.000000e+00 1033.0
9 TraesCS1D01G254800 chr1A 90.854 164 9 5 5063 5221 447639480 447639318 1.140000e-51 215.0
10 TraesCS1D01G254800 chr1A 97.674 43 1 0 2637 2679 447642547 447642505 2.020000e-09 75.0
11 TraesCS1D01G254800 chr6B 96.471 85 3 0 4974 5058 646750143 646750059 1.960000e-29 141.0
12 TraesCS1D01G254800 chr2D 92.857 98 5 1 4970 5065 128890635 128890732 1.960000e-29 141.0
13 TraesCS1D01G254800 chr2B 95.455 88 4 0 4971 5058 166044571 166044484 1.960000e-29 141.0
14 TraesCS1D01G254800 chr2B 92.000 100 6 2 4967 5066 73555176 73555079 7.050000e-29 139.0
15 TraesCS1D01G254800 chr3B 92.632 95 7 0 4967 5061 435816885 435816979 2.540000e-28 137.0
16 TraesCS1D01G254800 chr6D 92.632 95 5 1 4967 5061 113614161 113614069 9.120000e-28 135.0
17 TraesCS1D01G254800 chr3D 92.473 93 7 0 4969 5061 382751615 382751707 3.280000e-27 134.0
18 TraesCS1D01G254800 chr3D 91.579 95 8 0 4964 5058 450878880 450878786 1.180000e-26 132.0
19 TraesCS1D01G254800 chr5B 88.073 109 10 3 4952 5058 603648400 603648293 5.490000e-25 126.0


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 TraesCS1D01G254800 chr1D 347215144 347220364 5220 True 9642.00 9642 100.0000 1 5221 1 chr1D.!!$R1 5220
1 TraesCS1D01G254800 chr1B 467926794 467934992 8198 True 1463.04 6421 91.0850 182 5219 5 chr1B.!!$R1 5037
2 TraesCS1D01G254800 chr1A 447639318 447644891 5573 True 1434.20 3173 93.8358 276 5221 5 chr1A.!!$R1 4945

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
168 169 0.035630 ACTGAGAATGGGCTGCTCAC 60.036 55.0 3.32 0.00 35.09 3.51 F
1424 1557 0.108329 GTACGTGCATACCTGTGGCT 60.108 55.0 0.00 0.00 0.00 4.75 F
2381 2521 0.537143 TCTGTTTGATTGCGTGGGCT 60.537 50.0 0.00 0.00 40.82 5.19 F
2852 2997 0.179145 ACTACGACGGCATGCTGTAC 60.179 55.0 31.49 21.95 35.39 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 2050 0.035152 AACTCATGCGAGGCCATTGA 60.035 50.0 5.01 0.0 44.17 2.57 R
2437 2577 0.461548 CACCAAGCTCTCGGCATAGA 59.538 55.0 0.00 0.0 44.79 1.98 R
4112 4262 0.187117 TCCATGGCCACCTTGTTTCA 59.813 50.0 8.16 0.0 0.00 2.69 R
4627 4852 0.179023 TGCAGCACACCTGATCACAA 60.179 50.0 0.00 0.0 44.64 3.33 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
19 20 0.250234 TTCTGGCCATCTCCTTGACG 59.750 55.000 5.51 0.00 0.00 4.35
20 21 1.817099 CTGGCCATCTCCTTGACGC 60.817 63.158 5.51 0.00 0.00 5.19
21 22 2.892425 GGCCATCTCCTTGACGCG 60.892 66.667 3.53 3.53 0.00 6.01
22 23 2.892425 GCCATCTCCTTGACGCGG 60.892 66.667 12.47 0.00 0.00 6.46
23 24 2.579201 CCATCTCCTTGACGCGGT 59.421 61.111 12.47 0.00 0.00 5.68
24 25 1.811266 CCATCTCCTTGACGCGGTG 60.811 63.158 12.47 0.00 0.00 4.94
25 26 1.215382 CATCTCCTTGACGCGGTGA 59.785 57.895 12.47 0.00 0.00 4.02
26 27 0.803768 CATCTCCTTGACGCGGTGAG 60.804 60.000 12.47 8.60 0.00 3.51
27 28 1.949847 ATCTCCTTGACGCGGTGAGG 61.950 60.000 12.47 14.19 0.00 3.86
28 29 2.915659 TCCTTGACGCGGTGAGGT 60.916 61.111 12.47 0.00 0.00 3.85
29 30 2.030562 CCTTGACGCGGTGAGGTT 59.969 61.111 12.47 0.00 0.00 3.50
30 31 2.317609 CCTTGACGCGGTGAGGTTG 61.318 63.158 12.47 0.00 0.00 3.77
31 32 2.280524 TTGACGCGGTGAGGTTGG 60.281 61.111 12.47 0.00 0.00 3.77
32 33 3.818121 TTGACGCGGTGAGGTTGGG 62.818 63.158 12.47 0.00 0.00 4.12
35 36 4.636435 CGCGGTGAGGTTGGGGTT 62.636 66.667 0.00 0.00 0.00 4.11
36 37 2.203437 GCGGTGAGGTTGGGGTTT 60.203 61.111 0.00 0.00 0.00 3.27
37 38 2.265904 GCGGTGAGGTTGGGGTTTC 61.266 63.158 0.00 0.00 0.00 2.78
38 39 1.454539 CGGTGAGGTTGGGGTTTCT 59.545 57.895 0.00 0.00 0.00 2.52
39 40 0.179001 CGGTGAGGTTGGGGTTTCTT 60.179 55.000 0.00 0.00 0.00 2.52
40 41 1.328279 GGTGAGGTTGGGGTTTCTTG 58.672 55.000 0.00 0.00 0.00 3.02
41 42 1.411074 GGTGAGGTTGGGGTTTCTTGT 60.411 52.381 0.00 0.00 0.00 3.16
42 43 1.681264 GTGAGGTTGGGGTTTCTTGTG 59.319 52.381 0.00 0.00 0.00 3.33
43 44 1.566703 TGAGGTTGGGGTTTCTTGTGA 59.433 47.619 0.00 0.00 0.00 3.58
44 45 2.230660 GAGGTTGGGGTTTCTTGTGAG 58.769 52.381 0.00 0.00 0.00 3.51
45 46 1.133482 AGGTTGGGGTTTCTTGTGAGG 60.133 52.381 0.00 0.00 0.00 3.86
46 47 1.411074 GGTTGGGGTTTCTTGTGAGGT 60.411 52.381 0.00 0.00 0.00 3.85
47 48 1.681264 GTTGGGGTTTCTTGTGAGGTG 59.319 52.381 0.00 0.00 0.00 4.00
48 49 0.184933 TGGGGTTTCTTGTGAGGTGG 59.815 55.000 0.00 0.00 0.00 4.61
49 50 1.179174 GGGGTTTCTTGTGAGGTGGC 61.179 60.000 0.00 0.00 0.00 5.01
50 51 1.515521 GGGTTTCTTGTGAGGTGGCG 61.516 60.000 0.00 0.00 0.00 5.69
51 52 0.534203 GGTTTCTTGTGAGGTGGCGA 60.534 55.000 0.00 0.00 0.00 5.54
52 53 0.868406 GTTTCTTGTGAGGTGGCGAG 59.132 55.000 0.00 0.00 0.00 5.03
53 54 0.756294 TTTCTTGTGAGGTGGCGAGA 59.244 50.000 0.00 0.00 0.00 4.04
54 55 0.976641 TTCTTGTGAGGTGGCGAGAT 59.023 50.000 0.00 0.00 0.00 2.75
55 56 0.976641 TCTTGTGAGGTGGCGAGATT 59.023 50.000 0.00 0.00 0.00 2.40
56 57 1.347707 TCTTGTGAGGTGGCGAGATTT 59.652 47.619 0.00 0.00 0.00 2.17
57 58 1.466167 CTTGTGAGGTGGCGAGATTTG 59.534 52.381 0.00 0.00 0.00 2.32
58 59 0.321564 TGTGAGGTGGCGAGATTTGG 60.322 55.000 0.00 0.00 0.00 3.28
59 60 0.321653 GTGAGGTGGCGAGATTTGGT 60.322 55.000 0.00 0.00 0.00 3.67
60 61 0.321564 TGAGGTGGCGAGATTTGGTG 60.322 55.000 0.00 0.00 0.00 4.17
61 62 0.321653 GAGGTGGCGAGATTTGGTGT 60.322 55.000 0.00 0.00 0.00 4.16
62 63 0.321653 AGGTGGCGAGATTTGGTGTC 60.322 55.000 0.00 0.00 0.00 3.67
63 64 0.605319 GGTGGCGAGATTTGGTGTCA 60.605 55.000 0.00 0.00 0.00 3.58
64 65 0.517316 GTGGCGAGATTTGGTGTCAC 59.483 55.000 0.00 0.00 0.00 3.67
65 66 0.107643 TGGCGAGATTTGGTGTCACA 59.892 50.000 5.12 0.00 0.00 3.58
66 67 1.271325 TGGCGAGATTTGGTGTCACAT 60.271 47.619 5.12 0.00 0.00 3.21
67 68 1.131126 GGCGAGATTTGGTGTCACATG 59.869 52.381 5.12 0.00 0.00 3.21
68 69 1.466360 GCGAGATTTGGTGTCACATGC 60.466 52.381 5.12 0.00 0.00 4.06
69 70 2.079158 CGAGATTTGGTGTCACATGCT 58.921 47.619 5.12 0.00 0.00 3.79
70 71 2.159612 CGAGATTTGGTGTCACATGCTG 60.160 50.000 5.12 0.00 0.00 4.41
71 72 2.816087 GAGATTTGGTGTCACATGCTGT 59.184 45.455 5.12 0.00 0.00 4.40
72 73 4.002982 GAGATTTGGTGTCACATGCTGTA 58.997 43.478 5.12 0.00 0.00 2.74
73 74 4.005650 AGATTTGGTGTCACATGCTGTAG 58.994 43.478 5.12 0.00 0.00 2.74
74 75 3.483808 TTTGGTGTCACATGCTGTAGA 57.516 42.857 5.12 0.00 0.00 2.59
75 76 3.701205 TTGGTGTCACATGCTGTAGAT 57.299 42.857 5.12 0.00 0.00 1.98
76 77 3.251479 TGGTGTCACATGCTGTAGATC 57.749 47.619 5.12 0.00 0.00 2.75
77 78 2.833943 TGGTGTCACATGCTGTAGATCT 59.166 45.455 5.12 0.00 0.00 2.75
78 79 4.023291 TGGTGTCACATGCTGTAGATCTA 58.977 43.478 5.12 0.00 0.00 1.98
79 80 4.651045 TGGTGTCACATGCTGTAGATCTAT 59.349 41.667 5.57 0.00 0.00 1.98
80 81 5.129320 TGGTGTCACATGCTGTAGATCTATT 59.871 40.000 5.57 0.00 0.00 1.73
81 82 5.694006 GGTGTCACATGCTGTAGATCTATTC 59.306 44.000 5.57 0.00 0.00 1.75
82 83 6.276091 GTGTCACATGCTGTAGATCTATTCA 58.724 40.000 5.57 5.02 0.00 2.57
83 84 6.420306 GTGTCACATGCTGTAGATCTATTCAG 59.580 42.308 13.53 13.53 0.00 3.02
84 85 5.925397 GTCACATGCTGTAGATCTATTCAGG 59.075 44.000 17.55 13.72 0.00 3.86
85 86 5.835280 TCACATGCTGTAGATCTATTCAGGA 59.165 40.000 17.55 15.99 33.36 3.86
86 87 6.015603 TCACATGCTGTAGATCTATTCAGGAG 60.016 42.308 17.55 12.50 32.47 3.69
87 88 5.837979 ACATGCTGTAGATCTATTCAGGAGT 59.162 40.000 17.55 12.94 32.47 3.85
88 89 6.326064 ACATGCTGTAGATCTATTCAGGAGTT 59.674 38.462 17.55 7.11 32.47 3.01
89 90 6.398234 TGCTGTAGATCTATTCAGGAGTTC 57.602 41.667 17.55 5.66 0.00 3.01
90 91 5.893824 TGCTGTAGATCTATTCAGGAGTTCA 59.106 40.000 17.55 7.57 0.00 3.18
91 92 6.381133 TGCTGTAGATCTATTCAGGAGTTCAA 59.619 38.462 17.55 0.00 0.00 2.69
92 93 6.699642 GCTGTAGATCTATTCAGGAGTTCAAC 59.300 42.308 17.55 0.35 0.00 3.18
93 94 6.796426 TGTAGATCTATTCAGGAGTTCAACG 58.204 40.000 5.57 0.00 0.00 4.10
94 95 4.688021 AGATCTATTCAGGAGTTCAACGC 58.312 43.478 0.00 0.00 0.00 4.84
95 96 3.247006 TCTATTCAGGAGTTCAACGCC 57.753 47.619 1.20 1.20 38.44 5.68
96 97 1.927174 CTATTCAGGAGTTCAACGCCG 59.073 52.381 4.45 0.46 43.27 6.46
97 98 0.320374 ATTCAGGAGTTCAACGCCGA 59.680 50.000 4.45 2.92 43.27 5.54
98 99 0.599204 TTCAGGAGTTCAACGCCGAC 60.599 55.000 4.45 0.00 43.27 4.79
99 100 2.049433 AGGAGTTCAACGCCGACG 60.049 61.111 4.45 0.00 43.27 5.12
100 101 2.049802 GGAGTTCAACGCCGACGA 60.050 61.111 0.00 0.00 43.93 4.20
101 102 2.370393 GGAGTTCAACGCCGACGAC 61.370 63.158 0.00 0.00 43.93 4.34
102 103 1.371389 GAGTTCAACGCCGACGACT 60.371 57.895 0.00 0.00 43.93 4.18
103 104 1.606350 GAGTTCAACGCCGACGACTG 61.606 60.000 0.00 0.00 43.93 3.51
104 105 3.033764 TTCAACGCCGACGACTGC 61.034 61.111 0.00 0.00 43.93 4.40
111 112 2.809174 CCGACGACTGCGCATGAA 60.809 61.111 12.24 0.00 42.48 2.57
112 113 2.379634 CCGACGACTGCGCATGAAA 61.380 57.895 12.24 0.00 42.48 2.69
113 114 1.491127 CGACGACTGCGCATGAAAA 59.509 52.632 12.24 0.00 42.48 2.29
114 115 0.110867 CGACGACTGCGCATGAAAAA 60.111 50.000 12.24 0.00 42.48 1.94
115 116 1.318251 GACGACTGCGCATGAAAAAC 58.682 50.000 12.24 0.00 42.48 2.43
116 117 0.944386 ACGACTGCGCATGAAAAACT 59.056 45.000 12.24 0.00 42.48 2.66
117 118 1.333619 ACGACTGCGCATGAAAAACTT 59.666 42.857 12.24 0.00 42.48 2.66
118 119 1.971962 CGACTGCGCATGAAAAACTTC 59.028 47.619 12.24 0.00 0.00 3.01
119 120 2.319472 GACTGCGCATGAAAAACTTCC 58.681 47.619 12.24 0.00 0.00 3.46
120 121 1.680735 ACTGCGCATGAAAAACTTCCA 59.319 42.857 12.24 0.00 0.00 3.53
121 122 2.287788 ACTGCGCATGAAAAACTTCCAG 60.288 45.455 12.24 0.00 0.00 3.86
122 123 1.063031 GCGCATGAAAAACTTCCAGC 58.937 50.000 0.30 0.00 0.00 4.85
123 124 1.336240 GCGCATGAAAAACTTCCAGCT 60.336 47.619 0.30 0.00 0.00 4.24
124 125 2.322161 CGCATGAAAAACTTCCAGCTG 58.678 47.619 6.78 6.78 0.00 4.24
125 126 2.287788 CGCATGAAAAACTTCCAGCTGT 60.288 45.455 13.81 0.00 0.00 4.40
126 127 3.311966 GCATGAAAAACTTCCAGCTGTC 58.688 45.455 13.81 1.12 0.00 3.51
127 128 3.243501 GCATGAAAAACTTCCAGCTGTCA 60.244 43.478 13.81 7.41 0.00 3.58
128 129 4.560108 GCATGAAAAACTTCCAGCTGTCAT 60.560 41.667 13.81 9.50 0.00 3.06
129 130 5.535333 CATGAAAAACTTCCAGCTGTCATT 58.465 37.500 13.81 0.00 0.00 2.57
130 131 6.680810 CATGAAAAACTTCCAGCTGTCATTA 58.319 36.000 13.81 0.00 0.00 1.90
131 132 6.317789 TGAAAAACTTCCAGCTGTCATTAG 57.682 37.500 13.81 4.76 0.00 1.73
132 133 6.061441 TGAAAAACTTCCAGCTGTCATTAGA 58.939 36.000 13.81 0.00 0.00 2.10
133 134 6.545666 TGAAAAACTTCCAGCTGTCATTAGAA 59.454 34.615 13.81 6.81 0.00 2.10
134 135 6.959639 AAAACTTCCAGCTGTCATTAGAAA 57.040 33.333 13.81 0.00 0.00 2.52
135 136 7.530426 AAAACTTCCAGCTGTCATTAGAAAT 57.470 32.000 13.81 0.00 0.00 2.17
136 137 8.635765 AAAACTTCCAGCTGTCATTAGAAATA 57.364 30.769 13.81 0.00 0.00 1.40
137 138 7.617041 AACTTCCAGCTGTCATTAGAAATAC 57.383 36.000 13.81 0.00 0.00 1.89
138 139 6.116126 ACTTCCAGCTGTCATTAGAAATACC 58.884 40.000 13.81 0.00 0.00 2.73
139 140 5.957771 TCCAGCTGTCATTAGAAATACCT 57.042 39.130 13.81 0.00 0.00 3.08
140 141 6.313519 TCCAGCTGTCATTAGAAATACCTT 57.686 37.500 13.81 0.00 0.00 3.50
141 142 6.721318 TCCAGCTGTCATTAGAAATACCTTT 58.279 36.000 13.81 0.00 0.00 3.11
142 143 7.175104 TCCAGCTGTCATTAGAAATACCTTTT 58.825 34.615 13.81 0.00 0.00 2.27
143 144 7.669722 TCCAGCTGTCATTAGAAATACCTTTTT 59.330 33.333 13.81 0.00 0.00 1.94
161 162 4.759516 TTTTTCGTAACTGAGAATGGGC 57.240 40.909 0.00 0.00 0.00 5.36
162 163 3.695830 TTTCGTAACTGAGAATGGGCT 57.304 42.857 0.00 0.00 0.00 5.19
163 164 2.672961 TCGTAACTGAGAATGGGCTG 57.327 50.000 0.00 0.00 0.00 4.85
164 165 1.009829 CGTAACTGAGAATGGGCTGC 58.990 55.000 0.00 0.00 0.00 5.25
165 166 1.406069 CGTAACTGAGAATGGGCTGCT 60.406 52.381 0.00 0.00 0.00 4.24
166 167 2.284190 GTAACTGAGAATGGGCTGCTC 58.716 52.381 0.00 0.00 0.00 4.26
167 168 0.694771 AACTGAGAATGGGCTGCTCA 59.305 50.000 3.90 3.90 37.17 4.26
168 169 0.035630 ACTGAGAATGGGCTGCTCAC 60.036 55.000 3.32 0.00 35.09 3.51
169 170 1.078918 TGAGAATGGGCTGCTCACG 60.079 57.895 3.32 0.00 34.02 4.35
170 171 2.437359 AGAATGGGCTGCTCACGC 60.437 61.111 3.32 0.00 0.00 5.34
171 172 3.869272 GAATGGGCTGCTCACGCG 61.869 66.667 3.32 3.53 39.65 6.01
172 173 4.704833 AATGGGCTGCTCACGCGT 62.705 61.111 5.58 5.58 39.65 6.01
173 174 3.309436 AATGGGCTGCTCACGCGTA 62.309 57.895 13.44 0.00 39.65 4.42
174 175 4.735132 TGGGCTGCTCACGCGTAC 62.735 66.667 13.44 5.12 39.65 3.67
176 177 4.735132 GGCTGCTCACGCGTACCA 62.735 66.667 13.44 8.52 39.65 3.25
177 178 3.479269 GCTGCTCACGCGTACCAC 61.479 66.667 13.44 2.14 39.65 4.16
178 179 3.172575 CTGCTCACGCGTACCACG 61.173 66.667 13.44 0.00 45.88 4.94
233 234 6.573434 CACGCTATGATTCTTGGCCTATATA 58.427 40.000 3.32 0.00 0.00 0.86
261 262 6.613755 TTTCAAGTAGTTGTACTGCTTTCC 57.386 37.500 10.08 0.00 46.60 3.13
262 263 4.638304 TCAAGTAGTTGTACTGCTTTCCC 58.362 43.478 10.08 0.00 46.60 3.97
263 264 4.347000 TCAAGTAGTTGTACTGCTTTCCCT 59.653 41.667 10.08 0.00 46.60 4.20
264 265 5.541101 TCAAGTAGTTGTACTGCTTTCCCTA 59.459 40.000 10.08 0.00 46.60 3.53
265 266 6.042322 TCAAGTAGTTGTACTGCTTTCCCTAA 59.958 38.462 10.08 0.00 46.60 2.69
266 267 6.622427 AGTAGTTGTACTGCTTTCCCTAAT 57.378 37.500 0.00 0.00 37.96 1.73
272 273 8.793592 AGTTGTACTGCTTTCCCTAATAAAAAG 58.206 33.333 0.00 0.00 34.00 2.27
281 282 9.355215 GCTTTCCCTAATAAAAAGAAAAGTAGC 57.645 33.333 0.00 0.00 32.89 3.58
282 283 9.856488 CTTTCCCTAATAAAAAGAAAAGTAGCC 57.144 33.333 0.00 0.00 32.89 3.93
300 301 2.893398 GTACTGCCTCACCCCTCG 59.107 66.667 0.00 0.00 0.00 4.63
330 331 4.819105 AATTGGATTCGTGACTCTACCA 57.181 40.909 0.00 0.00 0.00 3.25
415 427 1.966451 CAGGAAACGGACCCACTGC 60.966 63.158 0.00 0.00 0.00 4.40
449 466 3.541093 AACAGTAACGCGACGCCGA 62.541 57.895 15.93 0.00 38.22 5.54
814 912 4.760204 AGCAAAACCGTATGATAATAGCCC 59.240 41.667 0.00 0.00 0.00 5.19
953 1063 3.589654 CTTGCCAGCGACGGAAGGA 62.590 63.158 0.00 0.00 0.00 3.36
958 1068 4.083862 AGCGACGGAAGGAAGGGC 62.084 66.667 0.00 0.00 0.00 5.19
967 1082 1.229529 AAGGAAGGGCGGAGAGGAA 60.230 57.895 0.00 0.00 0.00 3.36
1329 1462 3.878519 GCCGAGGAGGACGACGAG 61.879 72.222 0.00 0.00 45.00 4.18
1413 1546 4.338710 GGCAAGGGGGTACGTGCA 62.339 66.667 5.86 0.00 45.67 4.57
1424 1557 0.108329 GTACGTGCATACCTGTGGCT 60.108 55.000 0.00 0.00 0.00 4.75
1643 1776 7.095816 GGGAAAATTACCAAAGTTGTTTCATCG 60.096 37.037 4.40 0.00 0.00 3.84
1750 1883 9.881773 ATAGTATATTGGGTGGAATTTGATTGT 57.118 29.630 0.00 0.00 0.00 2.71
1826 1959 1.303561 ACAGGTGGACTACGGCGTA 60.304 57.895 19.80 19.80 0.00 4.42
1916 2049 2.368548 ACAGAACATCACTGTGGCACTA 59.631 45.455 19.83 4.41 45.19 2.74
1917 2050 3.008375 ACAGAACATCACTGTGGCACTAT 59.992 43.478 19.83 3.61 45.19 2.12
1918 2051 3.620374 CAGAACATCACTGTGGCACTATC 59.380 47.826 19.83 5.50 35.22 2.08
1919 2052 3.261643 AGAACATCACTGTGGCACTATCA 59.738 43.478 19.83 0.65 35.22 2.15
1959 2092 8.797438 AGTTTGGATTTAGAGTTCTTCATTTCC 58.203 33.333 0.00 0.00 0.00 3.13
1970 2103 7.665974 AGAGTTCTTCATTTCCGGTTTCTAATT 59.334 33.333 0.00 0.00 0.00 1.40
2122 2255 5.644977 TCTTTCTCAGAAACGATAGCTCA 57.355 39.130 0.00 0.00 42.67 4.26
2381 2521 0.537143 TCTGTTTGATTGCGTGGGCT 60.537 50.000 0.00 0.00 40.82 5.19
2446 2586 5.122519 TGTTGCATTTCTATTCTATGCCGA 58.877 37.500 0.00 0.00 43.01 5.54
2449 2589 5.233225 TGCATTTCTATTCTATGCCGAGAG 58.767 41.667 0.00 0.00 43.01 3.20
2482 2622 1.403679 CTGCTCTAGCGAACACTAGCT 59.596 52.381 0.00 0.00 45.83 3.32
2507 2647 3.794475 GCCCATCTTGCATGAGAAATTCG 60.794 47.826 8.40 0.00 0.00 3.34
2543 2683 5.107109 TGACGAAATTTCACAGGACAATG 57.893 39.130 17.99 0.54 0.00 2.82
2544 2684 4.578516 TGACGAAATTTCACAGGACAATGT 59.421 37.500 17.99 3.68 0.00 2.71
2556 2696 5.652014 CACAGGACAATGTTGTACCCAATAT 59.348 40.000 4.52 0.00 43.16 1.28
2681 2824 6.762661 CCAACAATTTTGGCCATCTAATTAGG 59.237 38.462 6.09 11.47 32.18 2.69
2687 2830 8.788238 ATTTTGGCCATCTAATTAGGAAGATT 57.212 30.769 6.09 0.00 29.93 2.40
2852 2997 0.179145 ACTACGACGGCATGCTGTAC 60.179 55.000 31.49 21.95 35.39 2.90
2860 3005 1.086696 GGCATGCTGTACGTGTTGAT 58.913 50.000 18.92 0.00 37.62 2.57
3079 3225 7.349598 ACATTCCTTGGCTGAAGAATTACTAT 58.650 34.615 0.00 0.00 32.82 2.12
3109 3255 6.039270 TCGGTTTTGATCACTTTGAAATGTCT 59.961 34.615 0.00 0.00 0.00 3.41
3145 3291 7.654022 TGGTTTTTCTGGTTTAGTTGATCTT 57.346 32.000 0.00 0.00 0.00 2.40
3268 3414 9.444600 TTTCCCAATACATTCTACTTCAGTTAC 57.555 33.333 0.00 0.00 0.00 2.50
3286 3432 4.214971 AGTTACGCTACAAAGAGAACTCGA 59.785 41.667 0.00 0.00 34.09 4.04
3331 3477 1.347707 TCAAGCGTCCTTGGAGTTCAT 59.652 47.619 3.86 0.00 46.69 2.57
3498 3644 7.781548 TCTTGTAGAAAACCTTACAACTCAC 57.218 36.000 0.00 0.00 0.00 3.51
3516 3662 6.349973 ACTCACTATTCGTGCATGTTATTG 57.650 37.500 5.68 5.02 43.46 1.90
3751 3897 8.589701 TCCCCTTCCTTTTAATCTGATAAAAC 57.410 34.615 0.00 0.00 32.77 2.43
3800 3947 6.880822 TCGACAATACTAACCAAATTCGAG 57.119 37.500 0.00 0.00 0.00 4.04
3841 3988 1.672356 CCTGGGTGGCGTTGAAGAG 60.672 63.158 0.00 0.00 0.00 2.85
3847 3994 1.608025 GGTGGCGTTGAAGAGACATCA 60.608 52.381 0.00 0.00 0.00 3.07
4001 4151 4.618489 GTGCAGTTTGATTTGCTGTATGAC 59.382 41.667 0.00 0.00 40.87 3.06
4073 4223 1.317613 TGCCAAACGAAGCAAGTCAT 58.682 45.000 0.00 0.00 35.69 3.06
4112 4262 5.959512 AGCATTCTAGGTAGTAGTGAGGAT 58.040 41.667 0.00 0.00 0.00 3.24
4194 4344 9.077885 ACTTGGATGTAACTTCAACATTGTAAT 57.922 29.630 0.00 0.00 37.69 1.89
4372 4574 5.514500 TTATCTATGACCTTAATGGGGCC 57.486 43.478 0.00 0.00 41.11 5.80
4377 4579 2.498441 TGACCTTAATGGGGCCTGTAT 58.502 47.619 0.84 0.00 41.11 2.29
4411 4624 2.357009 GCATCCATGGAGCTACTTTGTG 59.643 50.000 21.33 10.99 0.00 3.33
4483 4697 7.019774 TGTTTCAGAGAGTTTGTCATTTGAG 57.980 36.000 0.00 0.00 0.00 3.02
4516 4730 5.850046 ATTATAAGGGTTGGATCTCTGGG 57.150 43.478 0.00 0.00 0.00 4.45
4523 4737 1.134670 GTTGGATCTCTGGGGTCTTCG 60.135 57.143 0.00 0.00 0.00 3.79
4565 4779 4.214310 TCCATGGTTGTTGACTTGTCATT 58.786 39.130 12.58 0.00 0.00 2.57
4620 4845 2.578495 GCTTGTTGCGATTCTCTTGTG 58.422 47.619 0.00 0.00 0.00 3.33
4621 4846 2.224079 GCTTGTTGCGATTCTCTTGTGA 59.776 45.455 0.00 0.00 0.00 3.58
4622 4847 3.120060 GCTTGTTGCGATTCTCTTGTGAT 60.120 43.478 0.00 0.00 0.00 3.06
4623 4848 4.645956 CTTGTTGCGATTCTCTTGTGATC 58.354 43.478 0.00 0.00 0.00 2.92
4624 4849 3.002791 TGTTGCGATTCTCTTGTGATCC 58.997 45.455 0.00 0.00 0.00 3.36
4625 4850 3.265791 GTTGCGATTCTCTTGTGATCCT 58.734 45.455 0.00 0.00 0.00 3.24
4626 4851 3.170791 TGCGATTCTCTTGTGATCCTC 57.829 47.619 0.00 0.00 0.00 3.71
4627 4852 2.762887 TGCGATTCTCTTGTGATCCTCT 59.237 45.455 0.00 0.00 0.00 3.69
4628 4853 3.196469 TGCGATTCTCTTGTGATCCTCTT 59.804 43.478 0.00 0.00 0.00 2.85
4629 4854 3.555139 GCGATTCTCTTGTGATCCTCTTG 59.445 47.826 0.00 0.00 0.00 3.02
4630 4855 4.753233 CGATTCTCTTGTGATCCTCTTGT 58.247 43.478 0.00 0.00 0.00 3.16
4685 4910 1.577328 CCATCGTTTTCCGCTGCTGT 61.577 55.000 0.00 0.00 36.19 4.40
4806 5034 6.306199 TGTTGGATATATTTGTCCATGGGAG 58.694 40.000 13.02 0.00 42.11 4.30
4815 5043 6.780457 ATTTGTCCATGGGAGATAACTTTG 57.220 37.500 13.02 0.00 29.39 2.77
4920 8324 2.069273 CCGGCTCCGTGAATGAATATC 58.931 52.381 7.59 0.00 37.81 1.63
4928 8332 6.038714 GCTCCGTGAATGAATATCTTCCTTTT 59.961 38.462 0.00 0.00 0.00 2.27
5000 8405 9.495382 ACTCCCTCTGTAAAGAAATATAAGAGT 57.505 33.333 0.00 0.00 0.00 3.24
5001 8406 9.757227 CTCCCTCTGTAAAGAAATATAAGAGTG 57.243 37.037 0.00 0.00 0.00 3.51
5003 8408 9.892130 CCCTCTGTAAAGAAATATAAGAGTGTT 57.108 33.333 0.00 0.00 0.00 3.32
5149 9175 9.466497 AATTTAAAGTTGCCATCTCTATCTTCA 57.534 29.630 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.250234 CGTCAAGGAGATGGCCAGAA 59.750 55.000 13.05 0.00 0.00 3.02
2 3 1.817099 GCGTCAAGGAGATGGCCAG 60.817 63.158 13.05 0.00 33.68 4.85
3 4 2.268920 GCGTCAAGGAGATGGCCA 59.731 61.111 8.56 8.56 33.68 5.36
4 5 2.892425 CGCGTCAAGGAGATGGCC 60.892 66.667 0.00 0.00 33.68 5.36
5 6 2.892425 CCGCGTCAAGGAGATGGC 60.892 66.667 4.92 0.00 33.68 4.40
6 7 1.811266 CACCGCGTCAAGGAGATGG 60.811 63.158 4.92 0.00 33.68 3.51
7 8 0.803768 CTCACCGCGTCAAGGAGATG 60.804 60.000 4.92 0.00 36.29 2.90
8 9 1.513158 CTCACCGCGTCAAGGAGAT 59.487 57.895 4.92 0.00 0.00 2.75
10 11 2.125912 CCTCACCGCGTCAAGGAG 60.126 66.667 4.92 4.11 0.00 3.69
12 13 2.030562 AACCTCACCGCGTCAAGG 59.969 61.111 4.92 10.84 34.94 3.61
13 14 2.317609 CCAACCTCACCGCGTCAAG 61.318 63.158 4.92 0.00 0.00 3.02
18 19 4.636435 AACCCCAACCTCACCGCG 62.636 66.667 0.00 0.00 0.00 6.46
19 20 2.203437 AAACCCCAACCTCACCGC 60.203 61.111 0.00 0.00 0.00 5.68
20 21 0.179001 AAGAAACCCCAACCTCACCG 60.179 55.000 0.00 0.00 0.00 4.94
21 22 1.328279 CAAGAAACCCCAACCTCACC 58.672 55.000 0.00 0.00 0.00 4.02
22 23 1.681264 CACAAGAAACCCCAACCTCAC 59.319 52.381 0.00 0.00 0.00 3.51
23 24 1.566703 TCACAAGAAACCCCAACCTCA 59.433 47.619 0.00 0.00 0.00 3.86
24 25 2.230660 CTCACAAGAAACCCCAACCTC 58.769 52.381 0.00 0.00 0.00 3.85
25 26 1.133482 CCTCACAAGAAACCCCAACCT 60.133 52.381 0.00 0.00 0.00 3.50
26 27 1.328279 CCTCACAAGAAACCCCAACC 58.672 55.000 0.00 0.00 0.00 3.77
27 28 1.681264 CACCTCACAAGAAACCCCAAC 59.319 52.381 0.00 0.00 0.00 3.77
28 29 1.410932 CCACCTCACAAGAAACCCCAA 60.411 52.381 0.00 0.00 0.00 4.12
29 30 0.184933 CCACCTCACAAGAAACCCCA 59.815 55.000 0.00 0.00 0.00 4.96
30 31 1.179174 GCCACCTCACAAGAAACCCC 61.179 60.000 0.00 0.00 0.00 4.95
31 32 1.515521 CGCCACCTCACAAGAAACCC 61.516 60.000 0.00 0.00 0.00 4.11
32 33 0.534203 TCGCCACCTCACAAGAAACC 60.534 55.000 0.00 0.00 0.00 3.27
33 34 0.868406 CTCGCCACCTCACAAGAAAC 59.132 55.000 0.00 0.00 0.00 2.78
34 35 0.756294 TCTCGCCACCTCACAAGAAA 59.244 50.000 0.00 0.00 0.00 2.52
35 36 0.976641 ATCTCGCCACCTCACAAGAA 59.023 50.000 0.00 0.00 0.00 2.52
36 37 0.976641 AATCTCGCCACCTCACAAGA 59.023 50.000 0.00 0.00 0.00 3.02
37 38 1.466167 CAAATCTCGCCACCTCACAAG 59.534 52.381 0.00 0.00 0.00 3.16
38 39 1.522668 CAAATCTCGCCACCTCACAA 58.477 50.000 0.00 0.00 0.00 3.33
39 40 0.321564 CCAAATCTCGCCACCTCACA 60.322 55.000 0.00 0.00 0.00 3.58
40 41 0.321653 ACCAAATCTCGCCACCTCAC 60.322 55.000 0.00 0.00 0.00 3.51
41 42 0.321564 CACCAAATCTCGCCACCTCA 60.322 55.000 0.00 0.00 0.00 3.86
42 43 0.321653 ACACCAAATCTCGCCACCTC 60.322 55.000 0.00 0.00 0.00 3.85
43 44 0.321653 GACACCAAATCTCGCCACCT 60.322 55.000 0.00 0.00 0.00 4.00
44 45 0.605319 TGACACCAAATCTCGCCACC 60.605 55.000 0.00 0.00 0.00 4.61
45 46 0.517316 GTGACACCAAATCTCGCCAC 59.483 55.000 0.00 0.00 0.00 5.01
46 47 0.107643 TGTGACACCAAATCTCGCCA 59.892 50.000 2.45 0.00 0.00 5.69
47 48 1.131126 CATGTGACACCAAATCTCGCC 59.869 52.381 2.45 0.00 0.00 5.54
48 49 1.466360 GCATGTGACACCAAATCTCGC 60.466 52.381 2.45 0.00 0.00 5.03
49 50 2.079158 AGCATGTGACACCAAATCTCG 58.921 47.619 2.45 0.00 0.00 4.04
50 51 3.482722 CAGCATGTGACACCAAATCTC 57.517 47.619 2.45 0.00 0.00 2.75
64 65 6.343716 ACTCCTGAATAGATCTACAGCATG 57.656 41.667 4.10 4.77 46.00 4.06
65 66 6.552725 TGAACTCCTGAATAGATCTACAGCAT 59.447 38.462 4.10 0.00 0.00 3.79
66 67 5.893824 TGAACTCCTGAATAGATCTACAGCA 59.106 40.000 4.10 2.96 0.00 4.41
67 68 6.398234 TGAACTCCTGAATAGATCTACAGC 57.602 41.667 4.10 0.00 0.00 4.40
68 69 6.915300 CGTTGAACTCCTGAATAGATCTACAG 59.085 42.308 4.10 8.82 0.00 2.74
69 70 6.680625 GCGTTGAACTCCTGAATAGATCTACA 60.681 42.308 4.10 0.00 0.00 2.74
70 71 5.688176 GCGTTGAACTCCTGAATAGATCTAC 59.312 44.000 4.10 0.00 0.00 2.59
71 72 5.221263 GGCGTTGAACTCCTGAATAGATCTA 60.221 44.000 4.57 4.57 0.00 1.98
72 73 4.442192 GGCGTTGAACTCCTGAATAGATCT 60.442 45.833 0.00 0.00 0.00 2.75
73 74 3.804873 GGCGTTGAACTCCTGAATAGATC 59.195 47.826 0.00 0.00 0.00 2.75
74 75 3.738281 CGGCGTTGAACTCCTGAATAGAT 60.738 47.826 2.59 0.00 0.00 1.98
75 76 2.416836 CGGCGTTGAACTCCTGAATAGA 60.417 50.000 2.59 0.00 0.00 1.98
76 77 1.927174 CGGCGTTGAACTCCTGAATAG 59.073 52.381 2.59 0.00 0.00 1.73
77 78 1.546923 TCGGCGTTGAACTCCTGAATA 59.453 47.619 6.85 0.00 0.00 1.75
78 79 0.320374 TCGGCGTTGAACTCCTGAAT 59.680 50.000 6.85 0.00 0.00 2.57
79 80 0.599204 GTCGGCGTTGAACTCCTGAA 60.599 55.000 6.85 0.00 0.00 3.02
80 81 1.006571 GTCGGCGTTGAACTCCTGA 60.007 57.895 6.85 0.00 0.00 3.86
81 82 2.372690 CGTCGGCGTTGAACTCCTG 61.373 63.158 6.85 0.00 0.00 3.86
82 83 2.049433 CGTCGGCGTTGAACTCCT 60.049 61.111 6.85 0.00 0.00 3.69
83 84 2.049802 TCGTCGGCGTTGAACTCC 60.050 61.111 10.18 0.00 39.49 3.85
84 85 1.371389 AGTCGTCGGCGTTGAACTC 60.371 57.895 10.18 0.00 39.49 3.01
85 86 1.660575 CAGTCGTCGGCGTTGAACT 60.661 57.895 10.18 1.66 39.49 3.01
86 87 2.844146 CAGTCGTCGGCGTTGAAC 59.156 61.111 10.18 0.00 39.49 3.18
87 88 3.033764 GCAGTCGTCGGCGTTGAA 61.034 61.111 10.18 0.00 39.49 2.69
94 95 1.896339 TTTTCATGCGCAGTCGTCGG 61.896 55.000 18.32 0.00 38.14 4.79
95 96 0.110867 TTTTTCATGCGCAGTCGTCG 60.111 50.000 18.32 0.00 38.14 5.12
96 97 1.069906 AGTTTTTCATGCGCAGTCGTC 60.070 47.619 18.32 2.97 38.14 4.20
97 98 0.944386 AGTTTTTCATGCGCAGTCGT 59.056 45.000 18.32 0.00 38.14 4.34
98 99 1.971962 GAAGTTTTTCATGCGCAGTCG 59.028 47.619 18.32 7.12 34.53 4.18
99 100 2.287547 TGGAAGTTTTTCATGCGCAGTC 60.288 45.455 18.32 1.53 34.90 3.51
100 101 1.680735 TGGAAGTTTTTCATGCGCAGT 59.319 42.857 18.32 0.66 34.90 4.40
101 102 2.322161 CTGGAAGTTTTTCATGCGCAG 58.678 47.619 18.32 8.46 34.90 5.18
102 103 1.602668 GCTGGAAGTTTTTCATGCGCA 60.603 47.619 14.96 14.96 34.90 6.09
103 104 1.063031 GCTGGAAGTTTTTCATGCGC 58.937 50.000 0.00 0.00 34.90 6.09
104 105 2.287788 ACAGCTGGAAGTTTTTCATGCG 60.288 45.455 19.93 0.00 37.79 4.73
105 106 3.243501 TGACAGCTGGAAGTTTTTCATGC 60.244 43.478 19.93 0.00 34.90 4.06
106 107 4.572985 TGACAGCTGGAAGTTTTTCATG 57.427 40.909 19.93 0.00 34.90 3.07
107 108 5.796424 AATGACAGCTGGAAGTTTTTCAT 57.204 34.783 19.93 12.14 34.90 2.57
108 109 6.061441 TCTAATGACAGCTGGAAGTTTTTCA 58.939 36.000 19.93 10.22 34.90 2.69
109 110 6.560253 TCTAATGACAGCTGGAAGTTTTTC 57.440 37.500 19.93 4.13 35.30 2.29
110 111 6.959639 TTCTAATGACAGCTGGAAGTTTTT 57.040 33.333 19.93 4.33 35.30 1.94
111 112 6.959639 TTTCTAATGACAGCTGGAAGTTTT 57.040 33.333 19.93 5.37 35.30 2.43
112 113 7.121315 GGTATTTCTAATGACAGCTGGAAGTTT 59.879 37.037 19.93 6.76 35.30 2.66
113 114 6.599638 GGTATTTCTAATGACAGCTGGAAGTT 59.400 38.462 19.93 9.61 35.30 2.66
114 115 6.069963 AGGTATTTCTAATGACAGCTGGAAGT 60.070 38.462 19.93 9.66 35.30 3.01
115 116 6.352516 AGGTATTTCTAATGACAGCTGGAAG 58.647 40.000 19.93 7.61 0.00 3.46
116 117 6.313519 AGGTATTTCTAATGACAGCTGGAA 57.686 37.500 19.93 7.70 0.00 3.53
117 118 5.957771 AGGTATTTCTAATGACAGCTGGA 57.042 39.130 19.93 4.16 0.00 3.86
118 119 7.396540 AAAAGGTATTTCTAATGACAGCTGG 57.603 36.000 19.93 0.00 0.00 4.85
140 141 4.215399 CAGCCCATTCTCAGTTACGAAAAA 59.785 41.667 0.00 0.00 0.00 1.94
141 142 3.751175 CAGCCCATTCTCAGTTACGAAAA 59.249 43.478 0.00 0.00 0.00 2.29
142 143 3.334691 CAGCCCATTCTCAGTTACGAAA 58.665 45.455 0.00 0.00 0.00 3.46
143 144 2.935238 GCAGCCCATTCTCAGTTACGAA 60.935 50.000 0.00 0.00 0.00 3.85
144 145 1.405526 GCAGCCCATTCTCAGTTACGA 60.406 52.381 0.00 0.00 0.00 3.43
145 146 1.009829 GCAGCCCATTCTCAGTTACG 58.990 55.000 0.00 0.00 0.00 3.18
146 147 2.284190 GAGCAGCCCATTCTCAGTTAC 58.716 52.381 0.00 0.00 0.00 2.50
147 148 1.908619 TGAGCAGCCCATTCTCAGTTA 59.091 47.619 0.00 0.00 33.42 2.24
148 149 0.694771 TGAGCAGCCCATTCTCAGTT 59.305 50.000 0.00 0.00 33.42 3.16
149 150 0.035630 GTGAGCAGCCCATTCTCAGT 60.036 55.000 0.00 0.00 37.51 3.41
150 151 1.088340 CGTGAGCAGCCCATTCTCAG 61.088 60.000 0.00 0.00 37.51 3.35
151 152 1.078918 CGTGAGCAGCCCATTCTCA 60.079 57.895 0.00 0.00 34.78 3.27
152 153 3.805267 CGTGAGCAGCCCATTCTC 58.195 61.111 0.00 0.00 0.00 2.87
188 189 6.055231 GTGCTACACACTGTCATGTAAAAA 57.945 37.500 0.00 0.00 46.41 1.94
189 190 5.666969 GTGCTACACACTGTCATGTAAAA 57.333 39.130 0.00 0.00 46.41 1.52
204 205 3.457234 CCAAGAATCATAGCGTGCTACA 58.543 45.455 3.26 0.00 0.00 2.74
239 240 5.061179 GGGAAAGCAGTACAACTACTTGAA 58.939 41.667 0.00 0.00 32.44 2.69
246 247 8.700439 TTTTTATTAGGGAAAGCAGTACAACT 57.300 30.769 0.00 0.00 0.00 3.16
252 253 8.924303 ACTTTTCTTTTTATTAGGGAAAGCAGT 58.076 29.630 0.00 0.00 31.99 4.40
255 256 9.355215 GCTACTTTTCTTTTTATTAGGGAAAGC 57.645 33.333 0.00 0.00 31.99 3.51
256 257 9.856488 GGCTACTTTTCTTTTTATTAGGGAAAG 57.144 33.333 0.00 0.00 0.00 2.62
261 262 9.159364 AGTACGGCTACTTTTCTTTTTATTAGG 57.841 33.333 0.00 0.00 27.62 2.69
262 263 9.968743 CAGTACGGCTACTTTTCTTTTTATTAG 57.031 33.333 0.00 0.00 30.03 1.73
263 264 8.445493 GCAGTACGGCTACTTTTCTTTTTATTA 58.555 33.333 10.99 0.00 30.03 0.98
264 265 7.303261 GCAGTACGGCTACTTTTCTTTTTATT 58.697 34.615 10.99 0.00 30.03 1.40
265 266 6.128090 GGCAGTACGGCTACTTTTCTTTTTAT 60.128 38.462 17.57 0.00 37.17 1.40
266 267 5.179929 GGCAGTACGGCTACTTTTCTTTTTA 59.820 40.000 17.57 0.00 37.17 1.52
281 282 2.683933 AGGGGTGAGGCAGTACGG 60.684 66.667 0.00 0.00 0.00 4.02
282 283 2.893398 GAGGGGTGAGGCAGTACG 59.107 66.667 0.00 0.00 0.00 3.67
300 301 4.319901 GTCACGAATCCAATTTTTACACGC 59.680 41.667 0.00 0.00 0.00 5.34
330 331 3.945981 GAGAAGGTTCTCGAGGAGTTT 57.054 47.619 13.56 0.47 43.63 2.66
368 376 1.474320 CGTGGCTGGGAATTTCGGATA 60.474 52.381 0.00 0.00 0.00 2.59
369 377 0.748005 CGTGGCTGGGAATTTCGGAT 60.748 55.000 0.00 0.00 0.00 4.18
370 378 1.376683 CGTGGCTGGGAATTTCGGA 60.377 57.895 0.00 0.00 0.00 4.55
420 432 1.677300 TTACTGTTGGGCCATGGCG 60.677 57.895 29.90 17.38 43.06 5.69
421 433 1.890174 GTTACTGTTGGGCCATGGC 59.110 57.895 29.47 29.47 41.06 4.40
423 435 1.506262 GCGTTACTGTTGGGCCATG 59.494 57.895 7.26 3.33 0.00 3.66
807 905 3.825623 GGGCTGGGCTGGGCTATT 61.826 66.667 4.29 0.00 0.00 1.73
814 912 2.439553 TAACTTTGGGGGCTGGGCTG 62.440 60.000 0.00 0.00 0.00 4.85
953 1063 0.252284 TCTCTTTCCTCTCCGCCCTT 60.252 55.000 0.00 0.00 0.00 3.95
958 1068 4.995124 TCGTTTTATCTCTTTCCTCTCCG 58.005 43.478 0.00 0.00 0.00 4.63
967 1082 1.653151 GCGCCCTCGTTTTATCTCTT 58.347 50.000 0.00 0.00 38.14 2.85
1031 1146 1.118838 CGCAGGAAGAGGAAGAGGAT 58.881 55.000 0.00 0.00 0.00 3.24
1137 1267 1.383799 CACCAGGCCCAGGATGAAA 59.616 57.895 18.23 0.00 39.69 2.69
1413 1546 3.797353 CCCGCCAGCCACAGGTAT 61.797 66.667 0.00 0.00 0.00 2.73
1489 1622 3.421741 TGCGCGCAGATAATAAACAAAC 58.578 40.909 33.09 0.00 0.00 2.93
1666 1799 4.576216 TCAGGATAGCTCGTCAAGATTC 57.424 45.455 0.00 0.00 0.00 2.52
1750 1883 0.039618 GAGCCACCAGATTCCCCAAA 59.960 55.000 0.00 0.00 0.00 3.28
1826 1959 1.340405 CCATAAACCTGGCTGTGCTCT 60.340 52.381 0.00 0.00 0.00 4.09
1916 2049 0.182061 ACTCATGCGAGGCCATTGAT 59.818 50.000 5.01 0.00 44.17 2.57
1917 2050 0.035152 AACTCATGCGAGGCCATTGA 60.035 50.000 5.01 0.00 44.17 2.57
1918 2051 0.813184 AAACTCATGCGAGGCCATTG 59.187 50.000 5.01 0.00 44.17 2.82
1919 2052 0.813184 CAAACTCATGCGAGGCCATT 59.187 50.000 5.01 0.00 44.17 3.16
1959 2092 1.465689 CCTGCGCACAATTAGAAACCG 60.466 52.381 5.66 0.00 0.00 4.44
2122 2255 3.153919 ACATTCTACCGGCAACAACAAT 58.846 40.909 0.00 0.00 0.00 2.71
2239 2379 3.763897 ACCATCCATAGAAAAGCGCTTTT 59.236 39.130 40.19 40.19 44.59 2.27
2340 2480 0.961019 TGCCCAGTTTAGCTGCAAAG 59.039 50.000 1.02 0.00 43.71 2.77
2353 2493 2.159282 GCAATCAAACAGAGATGCCCAG 60.159 50.000 0.00 0.00 37.16 4.45
2356 2496 1.470098 ACGCAATCAAACAGAGATGCC 59.530 47.619 0.00 0.00 38.89 4.40
2437 2577 0.461548 CACCAAGCTCTCGGCATAGA 59.538 55.000 0.00 0.00 44.79 1.98
2438 2578 0.531532 CCACCAAGCTCTCGGCATAG 60.532 60.000 0.00 0.00 44.79 2.23
2439 2579 1.522092 CCACCAAGCTCTCGGCATA 59.478 57.895 0.00 0.00 44.79 3.14
2440 2580 2.270205 CCACCAAGCTCTCGGCAT 59.730 61.111 0.00 0.00 44.79 4.40
2441 2581 4.704833 GCCACCAAGCTCTCGGCA 62.705 66.667 10.57 0.00 44.79 5.69
2446 2586 1.677966 CAGCATGCCACCAAGCTCT 60.678 57.895 15.66 0.00 43.53 4.09
2507 2647 3.485947 TTCGTCATATTTTGGCAGCAC 57.514 42.857 0.00 0.00 0.00 4.40
2721 2864 9.639601 CTGACATTAGTATTGAACAGTGTTAGA 57.360 33.333 8.88 0.60 30.82 2.10
2852 2997 7.603297 AATTTTACGAGTTCAAATCAACACG 57.397 32.000 0.00 2.29 43.43 4.49
3079 3225 9.757227 ATTTCAAAGTGATCAAAACCGAAATTA 57.243 25.926 0.00 0.00 28.85 1.40
3109 3255 4.161377 CCAGAAAAACCAACTTTCCTCCAA 59.839 41.667 0.00 0.00 34.00 3.53
3145 3291 1.424638 GCCCAGTATTCCCTAGCAGA 58.575 55.000 0.00 0.00 0.00 4.26
3268 3414 3.181539 GCTTTCGAGTTCTCTTTGTAGCG 60.182 47.826 0.00 0.00 0.00 4.26
3286 3432 8.823220 ATGGTACTGTAATTCCAAATAGCTTT 57.177 30.769 0.00 0.00 33.55 3.51
3460 3606 7.770366 TTTCTACAAGATAAAAAGGGGGAAC 57.230 36.000 0.00 0.00 0.00 3.62
3498 3644 8.081208 AGAAGATCAATAACATGCACGAATAG 57.919 34.615 0.00 0.00 0.00 1.73
3751 3897 9.577110 AAACAAGAATTCATGCATAACTGTATG 57.423 29.630 10.49 0.00 44.23 2.39
3800 3947 8.122952 CAGGTTATCGTCCATTTGAATTTAGTC 58.877 37.037 0.00 0.00 0.00 2.59
3841 3988 3.665745 AGCACAAAAATGGGTGATGTC 57.334 42.857 0.00 0.00 37.18 3.06
3847 3994 3.938334 GTGAACAAAGCACAAAAATGGGT 59.062 39.130 0.00 0.00 36.31 4.51
4001 4151 2.276868 CAGCGCTCGAAAATGCCG 60.277 61.111 7.13 0.00 0.00 5.69
4112 4262 0.187117 TCCATGGCCACCTTGTTTCA 59.813 50.000 8.16 0.00 0.00 2.69
4194 4344 9.638239 GCTCAAATGGACAAATTAATTTACAGA 57.362 29.630 12.98 6.46 0.00 3.41
4411 4624 1.857837 CGTCAAAACCATTGCCAACAC 59.142 47.619 0.00 0.00 0.00 3.32
4483 4697 5.068591 CCAACCCTTATAATTGCTACCCAAC 59.931 44.000 0.00 0.00 35.99 3.77
4516 4730 1.135053 GGTCTAGCTTGTCCGAAGACC 60.135 57.143 12.61 12.61 46.78 3.85
4523 4737 5.437060 TGGATAATTTGGTCTAGCTTGTCC 58.563 41.667 4.61 4.61 0.00 4.02
4565 4779 4.573201 GTGCTTTGTTGGTACTGACACTTA 59.427 41.667 0.00 0.00 0.00 2.24
4620 4845 3.529533 CACACCTGATCACAAGAGGATC 58.470 50.000 5.02 0.00 41.20 3.36
4621 4846 2.355513 GCACACCTGATCACAAGAGGAT 60.356 50.000 5.02 0.00 0.00 3.24
4622 4847 1.002430 GCACACCTGATCACAAGAGGA 59.998 52.381 5.02 0.00 0.00 3.71
4623 4848 1.002888 AGCACACCTGATCACAAGAGG 59.997 52.381 0.00 0.00 0.00 3.69
4624 4849 2.074576 CAGCACACCTGATCACAAGAG 58.925 52.381 0.00 0.00 44.64 2.85
4625 4850 1.879372 GCAGCACACCTGATCACAAGA 60.879 52.381 0.00 0.00 44.64 3.02
4626 4851 0.520404 GCAGCACACCTGATCACAAG 59.480 55.000 0.00 0.00 44.64 3.16
4627 4852 0.179023 TGCAGCACACCTGATCACAA 60.179 50.000 0.00 0.00 44.64 3.33
4628 4853 0.886043 GTGCAGCACACCTGATCACA 60.886 55.000 21.22 0.00 44.64 3.58
4629 4854 1.871772 GTGCAGCACACCTGATCAC 59.128 57.895 21.22 0.00 44.64 3.06
4630 4855 4.384599 GTGCAGCACACCTGATCA 57.615 55.556 21.22 0.00 44.64 2.92
4685 4910 5.712917 ACCAGAAGTAGAAACCAAACAACAA 59.287 36.000 0.00 0.00 0.00 2.83
4796 5024 3.947834 CCACAAAGTTATCTCCCATGGAC 59.052 47.826 15.22 1.43 0.00 4.02
4806 5034 1.199097 CCACGCACCCACAAAGTTATC 59.801 52.381 0.00 0.00 0.00 1.75
4815 5043 3.041940 CTCGAACCACGCACCCAC 61.042 66.667 0.00 0.00 42.26 4.61
4928 8332 9.027202 GTATCATGGTTTCCTAAAAAGGGTAAA 57.973 33.333 0.00 0.00 0.00 2.01
4934 8338 9.401058 AGATCAGTATCATGGTTTCCTAAAAAG 57.599 33.333 0.00 0.00 34.28 2.27
4975 8380 9.757227 CACTCTTATATTTCTTTACAGAGGGAG 57.243 37.037 0.00 0.00 32.92 4.30
4976 8381 9.268282 ACACTCTTATATTTCTTTACAGAGGGA 57.732 33.333 2.59 0.00 34.50 4.20
4977 8382 9.892130 AACACTCTTATATTTCTTTACAGAGGG 57.108 33.333 0.00 0.00 36.55 4.30
5046 8451 8.750298 TCGATTTCTTTAATCTACTTCCTCTGT 58.250 33.333 0.00 0.00 40.46 3.41
5050 8455 9.720769 TGTTTCGATTTCTTTAATCTACTTCCT 57.279 29.630 0.00 0.00 40.46 3.36
5065 9086 7.643764 TCTGTTGATCACTTTTGTTTCGATTTC 59.356 33.333 0.00 0.00 0.00 2.17
5100 9121 3.003689 GCTTTGATGTAGCGCCAATGTAT 59.996 43.478 2.29 0.00 0.00 2.29
5108 9129 5.572896 ACTTTAAATTGCTTTGATGTAGCGC 59.427 36.000 0.00 0.00 41.54 5.92
5149 9175 5.479375 AGAAGAACATGAAGATGCAATTGGT 59.521 36.000 7.72 0.00 32.14 3.67


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

AutoCloner maintained by Alex Coulton.