Multiple sequence alignment - TraesCS3A01G165400

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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 TraesCS3A01G165400 chr3A 100.000 2715 0 0 1 2715 170487566 170484852 0.000000e+00 5014.0
1 TraesCS3A01G165400 chr3A 82.595 655 77 27 1104 1747 170391032 170390404 6.610000e-151 544.0
2 TraesCS3A01G165400 chr3A 82.022 178 24 6 1574 1747 170310536 170310709 7.830000e-31 145.0
3 TraesCS3A01G165400 chr3D 90.351 2280 138 33 458 2715 157659044 157661263 0.000000e+00 2916.0
4 TraesCS3A01G165400 chr3D 81.424 646 79 22 1104 1747 157750083 157750689 8.740000e-135 490.0
5 TraesCS3A01G165400 chr3D 87.288 354 36 6 145 494 157658081 157658429 1.960000e-106 396.0
6 TraesCS3A01G165400 chr3D 72.205 331 80 10 2381 2706 156992864 156993187 1.040000e-14 91.6
7 TraesCS3A01G165400 chr3B 92.883 1096 49 8 1068 2154 228983012 228984087 0.000000e+00 1565.0
8 TraesCS3A01G165400 chr3B 90.734 572 51 1 2144 2715 228994927 228995496 0.000000e+00 761.0
9 TraesCS3A01G165400 chr3B 88.663 591 39 11 469 1034 228982428 228983015 0.000000e+00 695.0
10 TraesCS3A01G165400 chr3B 82.335 651 91 17 1104 1747 229006306 229006939 6.610000e-151 544.0
11 TraesCS3A01G165400 chr3B 88.889 279 30 1 145 422 228977946 228978224 2.590000e-90 342.0
12 TraesCS3A01G165400 chr3B 88.462 52 5 1 2665 2715 684938648 684938597 8.120000e-06 62.1
13 TraesCS3A01G165400 chr3B 92.105 38 2 1 56 93 505839571 505839535 5.000000e-03 52.8
14 TraesCS3A01G165400 chr6D 79.152 566 58 25 1101 1664 438518592 438519099 1.200000e-88 337.0
15 TraesCS3A01G165400 chr7B 76.815 427 73 18 1109 1514 750391042 750390621 1.640000e-52 217.0
16 TraesCS3A01G165400 chr7A 76.651 424 73 17 1106 1508 732842273 732842691 7.620000e-51 211.0
17 TraesCS3A01G165400 chr7D 76.942 412 68 18 1124 1514 633695389 633694984 2.740000e-50 209.0
18 TraesCS3A01G165400 chrUn 82.022 178 24 6 1574 1747 293324337 293324510 7.830000e-31 145.0
19 TraesCS3A01G165400 chrUn 82.022 178 24 6 1574 1747 389790908 389791081 7.830000e-31 145.0
20 TraesCS3A01G165400 chr1B 71.515 330 80 13 2383 2706 2212729 2213050 2.900000e-10 76.8
21 TraesCS3A01G165400 chr4A 93.617 47 3 0 2669 2715 567056988 567056942 1.350000e-08 71.3


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 TraesCS3A01G165400 chr3A 170484852 170487566 2714 True 5014 5014 100.0000 1 2715 1 chr3A.!!$R2 2714
1 TraesCS3A01G165400 chr3A 170390404 170391032 628 True 544 544 82.5950 1104 1747 1 chr3A.!!$R1 643
2 TraesCS3A01G165400 chr3D 157658081 157661263 3182 False 1656 2916 88.8195 145 2715 2 chr3D.!!$F3 2570
3 TraesCS3A01G165400 chr3D 157750083 157750689 606 False 490 490 81.4240 1104 1747 1 chr3D.!!$F2 643
4 TraesCS3A01G165400 chr3B 228982428 228984087 1659 False 1130 1565 90.7730 469 2154 2 chr3B.!!$F4 1685
5 TraesCS3A01G165400 chr3B 228994927 228995496 569 False 761 761 90.7340 2144 2715 1 chr3B.!!$F2 571
6 TraesCS3A01G165400 chr3B 229006306 229006939 633 False 544 544 82.3350 1104 1747 1 chr3B.!!$F3 643
7 TraesCS3A01G165400 chr6D 438518592 438519099 507 False 337 337 79.1520 1101 1664 1 chr6D.!!$F1 563

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
136 137 0.044092 TGATAGAGGGTCAAGGGCCA 59.956 55.0 6.18 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2813 0.100861 GCTGGCGACCTAGTAGTGTC 59.899 60.0 8.11 8.11 0.0 3.67 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
22 23 2.995283 TGATGGAGAAATCTGTGCAGG 58.005 47.619 0.00 0.00 0.00 4.85
23 24 2.573009 TGATGGAGAAATCTGTGCAGGA 59.427 45.455 0.00 0.00 0.00 3.86
24 25 3.201487 TGATGGAGAAATCTGTGCAGGAT 59.799 43.478 0.00 0.00 0.00 3.24
25 26 4.409901 TGATGGAGAAATCTGTGCAGGATA 59.590 41.667 2.99 0.00 0.00 2.59
26 27 4.412796 TGGAGAAATCTGTGCAGGATAG 57.587 45.455 2.99 0.00 0.00 2.08
27 28 3.135348 TGGAGAAATCTGTGCAGGATAGG 59.865 47.826 2.99 0.00 0.00 2.57
28 29 3.135530 GGAGAAATCTGTGCAGGATAGGT 59.864 47.826 2.99 0.00 0.00 3.08
29 30 4.125703 GAGAAATCTGTGCAGGATAGGTG 58.874 47.826 2.99 0.00 0.00 4.00
30 31 3.521126 AGAAATCTGTGCAGGATAGGTGT 59.479 43.478 2.99 0.00 0.00 4.16
31 32 2.996249 ATCTGTGCAGGATAGGTGTG 57.004 50.000 0.00 0.00 0.00 3.82
32 33 1.644509 TCTGTGCAGGATAGGTGTGT 58.355 50.000 0.00 0.00 0.00 3.72
33 34 1.276138 TCTGTGCAGGATAGGTGTGTG 59.724 52.381 0.00 0.00 0.00 3.82
34 35 1.276138 CTGTGCAGGATAGGTGTGTGA 59.724 52.381 0.00 0.00 0.00 3.58
35 36 1.908619 TGTGCAGGATAGGTGTGTGAT 59.091 47.619 0.00 0.00 0.00 3.06
36 37 2.305635 TGTGCAGGATAGGTGTGTGATT 59.694 45.455 0.00 0.00 0.00 2.57
37 38 2.679837 GTGCAGGATAGGTGTGTGATTG 59.320 50.000 0.00 0.00 0.00 2.67
38 39 2.292267 GCAGGATAGGTGTGTGATTGG 58.708 52.381 0.00 0.00 0.00 3.16
39 40 2.356125 GCAGGATAGGTGTGTGATTGGT 60.356 50.000 0.00 0.00 0.00 3.67
40 41 3.273434 CAGGATAGGTGTGTGATTGGTG 58.727 50.000 0.00 0.00 0.00 4.17
41 42 2.912956 AGGATAGGTGTGTGATTGGTGT 59.087 45.455 0.00 0.00 0.00 4.16
42 43 3.055094 AGGATAGGTGTGTGATTGGTGTC 60.055 47.826 0.00 0.00 0.00 3.67
43 44 3.055094 GGATAGGTGTGTGATTGGTGTCT 60.055 47.826 0.00 0.00 0.00 3.41
44 45 2.550830 AGGTGTGTGATTGGTGTCTC 57.449 50.000 0.00 0.00 0.00 3.36
45 46 2.050144 AGGTGTGTGATTGGTGTCTCT 58.950 47.619 0.00 0.00 0.00 3.10
46 47 2.146342 GGTGTGTGATTGGTGTCTCTG 58.854 52.381 0.00 0.00 0.00 3.35
47 48 2.485479 GGTGTGTGATTGGTGTCTCTGT 60.485 50.000 0.00 0.00 0.00 3.41
48 49 2.802816 GTGTGTGATTGGTGTCTCTGTC 59.197 50.000 0.00 0.00 0.00 3.51
49 50 2.433970 TGTGTGATTGGTGTCTCTGTCA 59.566 45.455 0.00 0.00 0.00 3.58
50 51 3.062763 GTGTGATTGGTGTCTCTGTCAG 58.937 50.000 0.00 0.00 0.00 3.51
51 52 2.037641 TGTGATTGGTGTCTCTGTCAGG 59.962 50.000 0.00 0.00 0.00 3.86
52 53 2.037772 GTGATTGGTGTCTCTGTCAGGT 59.962 50.000 0.00 0.00 0.00 4.00
53 54 2.705658 TGATTGGTGTCTCTGTCAGGTT 59.294 45.455 0.00 0.00 0.00 3.50
54 55 2.620251 TTGGTGTCTCTGTCAGGTTG 57.380 50.000 0.00 0.00 0.00 3.77
55 56 1.496060 TGGTGTCTCTGTCAGGTTGT 58.504 50.000 0.00 0.00 0.00 3.32
56 57 1.837439 TGGTGTCTCTGTCAGGTTGTT 59.163 47.619 0.00 0.00 0.00 2.83
57 58 2.213499 GGTGTCTCTGTCAGGTTGTTG 58.787 52.381 0.00 0.00 0.00 3.33
58 59 2.420129 GGTGTCTCTGTCAGGTTGTTGT 60.420 50.000 0.00 0.00 0.00 3.32
59 60 3.270877 GTGTCTCTGTCAGGTTGTTGTT 58.729 45.455 0.00 0.00 0.00 2.83
60 61 3.309954 GTGTCTCTGTCAGGTTGTTGTTC 59.690 47.826 0.00 0.00 0.00 3.18
61 62 3.055458 TGTCTCTGTCAGGTTGTTGTTCA 60.055 43.478 0.00 0.00 0.00 3.18
62 63 4.130118 GTCTCTGTCAGGTTGTTGTTCAT 58.870 43.478 0.00 0.00 0.00 2.57
63 64 4.024556 GTCTCTGTCAGGTTGTTGTTCATG 60.025 45.833 0.00 0.00 0.00 3.07
64 65 3.213506 TCTGTCAGGTTGTTGTTCATGG 58.786 45.455 0.00 0.00 0.00 3.66
65 66 1.680735 TGTCAGGTTGTTGTTCATGGC 59.319 47.619 0.00 0.00 0.00 4.40
66 67 1.000274 GTCAGGTTGTTGTTCATGGCC 60.000 52.381 0.00 0.00 0.00 5.36
67 68 1.133513 TCAGGTTGTTGTTCATGGCCT 60.134 47.619 3.32 0.00 0.00 5.19
68 69 1.270550 CAGGTTGTTGTTCATGGCCTC 59.729 52.381 3.32 0.00 0.00 4.70
69 70 1.133513 AGGTTGTTGTTCATGGCCTCA 60.134 47.619 3.32 0.00 0.00 3.86
70 71 1.895131 GGTTGTTGTTCATGGCCTCAT 59.105 47.619 3.32 0.00 0.00 2.90
71 72 2.299867 GGTTGTTGTTCATGGCCTCATT 59.700 45.455 3.32 0.00 0.00 2.57
72 73 3.578688 GTTGTTGTTCATGGCCTCATTC 58.421 45.455 3.32 0.00 0.00 2.67
73 74 2.874014 TGTTGTTCATGGCCTCATTCA 58.126 42.857 3.32 0.00 0.00 2.57
74 75 3.433343 TGTTGTTCATGGCCTCATTCAT 58.567 40.909 3.32 0.00 0.00 2.57
75 76 3.444742 TGTTGTTCATGGCCTCATTCATC 59.555 43.478 3.32 0.00 0.00 2.92
76 77 3.369242 TGTTCATGGCCTCATTCATCA 57.631 42.857 3.32 0.00 0.00 3.07
77 78 3.905968 TGTTCATGGCCTCATTCATCAT 58.094 40.909 3.32 0.00 0.00 2.45
78 79 3.634910 TGTTCATGGCCTCATTCATCATG 59.365 43.478 3.32 0.00 37.23 3.07
79 80 2.871453 TCATGGCCTCATTCATCATGG 58.129 47.619 3.32 0.00 36.72 3.66
80 81 2.444010 TCATGGCCTCATTCATCATGGA 59.556 45.455 3.32 0.00 36.72 3.41
81 82 3.075432 TCATGGCCTCATTCATCATGGAT 59.925 43.478 3.32 0.00 36.72 3.41
82 83 3.605726 TGGCCTCATTCATCATGGATT 57.394 42.857 3.32 0.00 33.07 3.01
83 84 3.227614 TGGCCTCATTCATCATGGATTG 58.772 45.455 3.32 0.00 33.07 2.67
84 85 3.117436 TGGCCTCATTCATCATGGATTGA 60.117 43.478 3.32 0.00 39.12 2.57
85 86 3.893200 GGCCTCATTCATCATGGATTGAA 59.107 43.478 0.00 8.44 38.03 2.69
86 87 4.022242 GGCCTCATTCATCATGGATTGAAG 60.022 45.833 0.00 2.35 38.03 3.02
87 88 4.022242 GCCTCATTCATCATGGATTGAAGG 60.022 45.833 10.39 10.39 38.03 3.46
88 89 5.382616 CCTCATTCATCATGGATTGAAGGA 58.617 41.667 15.41 15.41 38.03 3.36
89 90 5.241064 CCTCATTCATCATGGATTGAAGGAC 59.759 44.000 13.49 0.00 38.03 3.85
90 91 5.757988 TCATTCATCATGGATTGAAGGACA 58.242 37.500 13.49 0.00 38.03 4.02
91 92 6.370453 TCATTCATCATGGATTGAAGGACAT 58.630 36.000 13.49 0.00 38.03 3.06
92 93 6.489022 TCATTCATCATGGATTGAAGGACATC 59.511 38.462 13.49 0.00 38.03 3.06
93 94 5.376756 TCATCATGGATTGAAGGACATCA 57.623 39.130 0.00 0.00 38.03 3.07
94 95 5.757988 TCATCATGGATTGAAGGACATCAA 58.242 37.500 0.00 0.00 43.03 2.57
105 106 7.757941 TTGAAGGACATCAATAACAATCACA 57.242 32.000 0.00 0.00 34.50 3.58
106 107 7.757941 TGAAGGACATCAATAACAATCACAA 57.242 32.000 0.00 0.00 0.00 3.33
107 108 8.175925 TGAAGGACATCAATAACAATCACAAA 57.824 30.769 0.00 0.00 0.00 2.83
108 109 8.805175 TGAAGGACATCAATAACAATCACAAAT 58.195 29.630 0.00 0.00 0.00 2.32
117 118 9.707957 TCAATAACAATCACAAATATAAGGGGT 57.292 29.630 0.00 0.00 0.00 4.95
118 119 9.748708 CAATAACAATCACAAATATAAGGGGTG 57.251 33.333 0.00 0.00 0.00 4.61
119 120 9.707957 AATAACAATCACAAATATAAGGGGTGA 57.292 29.630 0.00 0.00 42.07 4.02
122 123 8.924511 ACAATCACAAATATAAGGGGTGATAG 57.075 34.615 6.06 0.00 45.56 2.08
123 124 8.723365 ACAATCACAAATATAAGGGGTGATAGA 58.277 33.333 6.06 0.00 45.56 1.98
124 125 9.224267 CAATCACAAATATAAGGGGTGATAGAG 57.776 37.037 6.06 0.00 45.56 2.43
125 126 7.316393 TCACAAATATAAGGGGTGATAGAGG 57.684 40.000 0.00 0.00 33.88 3.69
126 127 6.272324 TCACAAATATAAGGGGTGATAGAGGG 59.728 42.308 0.00 0.00 33.88 4.30
127 128 6.044404 CACAAATATAAGGGGTGATAGAGGGT 59.956 42.308 0.00 0.00 0.00 4.34
128 129 6.272558 ACAAATATAAGGGGTGATAGAGGGTC 59.727 42.308 0.00 0.00 0.00 4.46
129 130 5.633473 ATATAAGGGGTGATAGAGGGTCA 57.367 43.478 0.00 0.00 0.00 4.02
130 131 2.661176 AAGGGGTGATAGAGGGTCAA 57.339 50.000 0.00 0.00 0.00 3.18
131 132 2.182516 AGGGGTGATAGAGGGTCAAG 57.817 55.000 0.00 0.00 0.00 3.02
132 133 1.132500 GGGGTGATAGAGGGTCAAGG 58.868 60.000 0.00 0.00 0.00 3.61
133 134 1.132500 GGGTGATAGAGGGTCAAGGG 58.868 60.000 0.00 0.00 0.00 3.95
134 135 0.470341 GGTGATAGAGGGTCAAGGGC 59.530 60.000 0.00 0.00 0.00 5.19
135 136 0.470341 GTGATAGAGGGTCAAGGGCC 59.530 60.000 0.00 0.00 0.00 5.80
136 137 0.044092 TGATAGAGGGTCAAGGGCCA 59.956 55.000 6.18 0.00 0.00 5.36
137 138 0.470341 GATAGAGGGTCAAGGGCCAC 59.530 60.000 6.18 0.00 0.00 5.01
138 139 0.253160 ATAGAGGGTCAAGGGCCACA 60.253 55.000 6.18 0.00 0.00 4.17
139 140 0.253160 TAGAGGGTCAAGGGCCACAT 60.253 55.000 6.18 0.00 0.00 3.21
140 141 1.379044 GAGGGTCAAGGGCCACATG 60.379 63.158 6.18 1.37 0.00 3.21
141 142 3.070576 GGGTCAAGGGCCACATGC 61.071 66.667 6.18 0.00 40.16 4.06
142 143 3.443045 GGTCAAGGGCCACATGCG 61.443 66.667 6.18 0.00 42.61 4.73
143 144 2.672996 GTCAAGGGCCACATGCGT 60.673 61.111 6.18 0.00 42.61 5.24
151 152 4.720902 CCACATGCGTGCCCTCCA 62.721 66.667 5.64 0.00 42.17 3.86
163 164 1.622499 CCCTCCAGGCCATCCAAAT 59.378 57.895 5.01 0.00 33.74 2.32
198 200 3.938334 ACATTTTTGTTGTCTGTTTGGGC 59.062 39.130 0.00 0.00 0.00 5.36
201 203 1.110442 TTGTTGTCTGTTTGGGCTGG 58.890 50.000 0.00 0.00 0.00 4.85
203 205 1.109323 GTTGTCTGTTTGGGCTGGCT 61.109 55.000 0.00 0.00 0.00 4.75
221 223 1.616994 GCTGGTTGGAGTTGCCCTAAT 60.617 52.381 0.00 0.00 34.97 1.73
236 238 4.526650 TGCCCTAATCAAGAAAAGAAACCC 59.473 41.667 0.00 0.00 0.00 4.11
246 248 6.607198 TCAAGAAAAGAAACCCTTCATTGTCT 59.393 34.615 0.00 0.00 33.02 3.41
254 256 2.034558 ACCCTTCATTGTCTTTGTTGCG 59.965 45.455 0.00 0.00 0.00 4.85
260 262 3.556365 TCATTGTCTTTGTTGCGTCGTTA 59.444 39.130 0.00 0.00 0.00 3.18
309 311 4.193826 TCCTTCTCTCCAACTTGAATCG 57.806 45.455 0.00 0.00 0.00 3.34
330 332 5.003160 TCGTGATCAAAGTGTCATGGATTT 58.997 37.500 0.00 0.00 33.29 2.17
333 335 6.963242 CGTGATCAAAGTGTCATGGATTTTAG 59.037 38.462 0.00 0.00 0.00 1.85
338 340 8.327941 TCAAAGTGTCATGGATTTTAGAAGAG 57.672 34.615 0.00 0.00 0.00 2.85
352 354 1.104630 GAAGAGAGTGGTACCCCTCG 58.895 60.000 17.45 0.00 32.88 4.63
356 358 2.108970 GAGAGTGGTACCCCTCGAATT 58.891 52.381 17.45 1.31 32.88 2.17
366 368 3.951663 ACCCCTCGAATTAAAACTCCAG 58.048 45.455 0.00 0.00 0.00 3.86
422 424 6.035843 GCTGATCAACTTGTTCACAGAAAAA 58.964 36.000 0.00 0.00 0.00 1.94
423 425 6.698766 GCTGATCAACTTGTTCACAGAAAAAT 59.301 34.615 0.00 0.00 0.00 1.82
426 428 8.249638 TGATCAACTTGTTCACAGAAAAATTCA 58.750 29.630 0.00 0.00 0.00 2.57
436 922 5.069781 TCACAGAAAAATTCAAACCGGGAAT 59.930 36.000 6.32 1.99 36.57 3.01
467 953 6.098679 GCAATTGCAACACCTTGTATTGATA 58.901 36.000 25.36 0.00 41.59 2.15
491 1142 3.260884 CCAAGTCCTTCTACCAGCAGTTA 59.739 47.826 0.00 0.00 0.00 2.24
508 1159 3.549471 CAGTTAGAGCAACGACTAGCATG 59.451 47.826 0.00 0.00 42.35 4.06
551 1202 4.460263 ACAGTGGCATTTGAGTTGACTTA 58.540 39.130 8.67 0.00 0.00 2.24
559 1218 7.014134 TGGCATTTGAGTTGACTTAATTTCTCA 59.986 33.333 0.00 0.00 0.00 3.27
613 1272 4.141801 CCTTGATTTCCTCGGGTACATACA 60.142 45.833 0.00 0.00 0.00 2.29
623 1282 1.944709 GGGTACATACACGGAATTGCC 59.055 52.381 0.00 0.00 0.00 4.52
648 1314 6.401474 CGTCTGTCGTTCTCATGATTGAAAAT 60.401 38.462 0.00 0.00 34.52 1.82
667 1333 0.814457 TGCAAGCGTGTTGGAACTTT 59.186 45.000 0.59 0.00 0.00 2.66
668 1334 1.199624 GCAAGCGTGTTGGAACTTTG 58.800 50.000 0.59 0.00 0.00 2.77
677 1343 1.760029 GTTGGAACTTTGAAAGGCCCA 59.240 47.619 10.02 12.28 34.00 5.36
759 1425 7.735326 ATTCGGTTAGGAAGCTATGGTATAT 57.265 36.000 0.00 0.00 0.00 0.86
767 1433 5.887035 AGGAAGCTATGGTATATCTACGGTC 59.113 44.000 0.00 0.00 0.00 4.79
768 1434 5.887035 GGAAGCTATGGTATATCTACGGTCT 59.113 44.000 0.00 0.00 0.00 3.85
772 1438 6.946583 AGCTATGGTATATCTACGGTCTCAAA 59.053 38.462 0.00 0.00 0.00 2.69
796 1462 0.109272 TCTTTCGACCAGTAGCAGCG 60.109 55.000 0.00 0.00 0.00 5.18
799 1465 1.934220 TTCGACCAGTAGCAGCGGAG 61.934 60.000 0.00 0.00 0.00 4.63
802 1468 2.185350 CCAGTAGCAGCGGAGTGG 59.815 66.667 9.21 9.21 0.00 4.00
836 1502 7.925043 ACACATCTAGTAGGAATATACTCCG 57.075 40.000 0.00 0.00 40.75 4.63
841 1507 7.180322 TCTAGTAGGAATATACTCCGACGAT 57.820 40.000 7.68 0.00 43.67 3.73
976 1644 4.719106 AGGAGTCCGCGTCGACCT 62.719 66.667 10.58 5.83 32.91 3.85
988 1657 1.202200 CGTCGACCTCAGATCCAAGAC 60.202 57.143 10.58 0.00 0.00 3.01
1018 1697 3.312421 CACCATGTCTAAGGTAATTGGCG 59.688 47.826 0.00 0.00 36.07 5.69
1041 1720 3.865745 ACCATATTCTTCGTTCTGCTTCG 59.134 43.478 0.00 0.00 0.00 3.79
1043 1722 2.086054 ATTCTTCGTTCTGCTTCGCT 57.914 45.000 0.00 0.00 0.00 4.93
1047 1726 0.032130 TTCGTTCTGCTTCGCTGTCT 59.968 50.000 0.00 0.00 0.00 3.41
1071 1750 1.479323 GAGGGTGTAGACATGCCGTTA 59.521 52.381 0.00 0.00 0.00 3.18
1089 1768 5.003402 GCCGTTACGATCATGAAAACATTTG 59.997 40.000 6.24 0.00 0.00 2.32
1090 1769 6.083630 CCGTTACGATCATGAAAACATTTGT 58.916 36.000 6.24 0.00 0.00 2.83
1091 1770 7.237871 CCGTTACGATCATGAAAACATTTGTA 58.762 34.615 6.24 0.00 0.00 2.41
1117 1796 6.991485 ACTGAATTTATGCTTGTGTTTTCG 57.009 33.333 0.00 0.00 0.00 3.46
1238 1948 4.487714 TCTCTCTCTGACTCTCTTCCTC 57.512 50.000 0.00 0.00 0.00 3.71
1244 1954 2.920271 TCTGACTCTCTTCCTCCCTGTA 59.080 50.000 0.00 0.00 0.00 2.74
1256 1966 1.273606 CTCCCTGTATATCCTGCACCG 59.726 57.143 0.00 0.00 0.00 4.94
1283 1995 4.033014 GCTGCTTCTCTTTACCGAATGTAC 59.967 45.833 0.00 0.00 0.00 2.90
1287 1999 4.100707 TCTCTTTACCGAATGTACGTGG 57.899 45.455 0.00 0.00 0.00 4.94
1321 2033 1.445582 GTCCATGGTGGTCGACGAC 60.446 63.158 21.05 21.05 39.03 4.34
1395 2108 0.528017 CAGCTGAGGAAGTCGTGCTA 59.472 55.000 8.42 0.00 36.28 3.49
1670 2431 1.524863 CTATGGCTACGGCTACGGCT 61.525 60.000 0.00 0.00 46.48 5.52
1671 2432 0.250858 TATGGCTACGGCTACGGCTA 60.251 55.000 0.00 0.00 46.48 3.93
1672 2433 1.803366 ATGGCTACGGCTACGGCTAC 61.803 60.000 0.00 0.00 46.48 3.58
1673 2434 2.051525 GCTACGGCTACGGCTACG 60.052 66.667 0.00 0.00 46.48 3.51
1674 2435 2.635899 CTACGGCTACGGCTACGG 59.364 66.667 0.00 0.00 46.48 4.02
1720 2490 1.064832 ACCTGGTACGAGTAGAGGTCC 60.065 57.143 0.00 0.00 30.98 4.46
1788 2558 1.142314 GGCGCGTATGTACCTGGAA 59.858 57.895 8.43 0.00 0.00 3.53
1825 2599 0.525311 TGTGTGTGCCTGTGTGTTTG 59.475 50.000 0.00 0.00 0.00 2.93
1828 2602 0.530288 GTGTGCCTGTGTGTTTGGTT 59.470 50.000 0.00 0.00 0.00 3.67
1855 2629 3.436704 AGTTCATATGCTTTGTGTCACGG 59.563 43.478 0.00 0.00 0.00 4.94
1867 2641 1.299089 GTCACGGTTGTTGGCTTGC 60.299 57.895 0.00 0.00 0.00 4.01
1887 2661 2.908634 CTGCAGTTTGCTTTCTGTACG 58.091 47.619 5.25 0.00 45.31 3.67
1978 2756 8.536175 ACAAAGTGAAAACCCAGAAAAAGATTA 58.464 29.630 0.00 0.00 0.00 1.75
1979 2757 9.546428 CAAAGTGAAAACCCAGAAAAAGATTAT 57.454 29.630 0.00 0.00 0.00 1.28
2070 2848 2.991540 GCCCCCACTGCCTTGTTC 60.992 66.667 0.00 0.00 0.00 3.18
2167 2946 4.642445 TTGTGCTTGATGCTATCATTGG 57.358 40.909 0.61 0.00 43.37 3.16
2181 2960 0.174845 CATTGGGCATGCAGGACTTG 59.825 55.000 21.36 5.16 0.00 3.16
2182 2961 0.040058 ATTGGGCATGCAGGACTTGA 59.960 50.000 21.36 0.00 0.00 3.02
2250 3029 7.775053 TTAGCTGACCCAACTTATGAAAAAT 57.225 32.000 0.00 0.00 0.00 1.82
2256 3035 9.143631 CTGACCCAACTTATGAAAAATTTGATC 57.856 33.333 0.00 0.00 0.00 2.92
2258 3037 7.096551 ACCCAACTTATGAAAAATTTGATCGG 58.903 34.615 0.00 0.00 0.00 4.18
2279 3058 3.149196 GGTCATGTGTTGTCCTGAATGT 58.851 45.455 0.00 0.00 31.54 2.71
2300 3079 3.192422 GTGAGGAGGGATATCATCTGTCG 59.808 52.174 4.83 0.00 31.39 4.35
2340 3119 4.762289 AGAGAAGTCTTTGACCACACTT 57.238 40.909 0.00 0.00 32.18 3.16
2404 3183 4.287067 AGATTTGAGAACTCTTGGGTGCTA 59.713 41.667 3.51 0.00 0.00 3.49
2514 3293 7.574607 AGAAACTTGAGGAAAAAGGTTAGAGA 58.425 34.615 0.00 0.00 34.72 3.10
2531 3310 7.337942 AGGTTAGAGAGTGGAATAAAAATGCAG 59.662 37.037 0.00 0.00 0.00 4.41
2615 3394 1.754803 CTGACGTCATGGGGCTTACTA 59.245 52.381 20.40 0.00 0.00 1.82
2616 3395 2.365617 CTGACGTCATGGGGCTTACTAT 59.634 50.000 20.40 0.00 0.00 2.12
2630 3409 7.126733 GGGGCTTACTATTGGAGATAGATAGA 58.873 42.308 0.40 0.00 0.00 1.98
2666 3445 2.100605 AGAGAACGATTGGCCAGAAC 57.899 50.000 5.11 0.22 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.201487 TCCTGCACAGATTTCTCCATCAT 59.799 43.478 0.00 0.00 0.00 2.45
3 4 3.272574 TCCTGCACAGATTTCTCCATC 57.727 47.619 0.00 0.00 0.00 3.51
4 5 3.947612 ATCCTGCACAGATTTCTCCAT 57.052 42.857 0.00 0.00 0.00 3.41
5 6 3.135348 CCTATCCTGCACAGATTTCTCCA 59.865 47.826 0.00 0.00 0.00 3.86
6 7 3.135530 ACCTATCCTGCACAGATTTCTCC 59.864 47.826 0.00 0.00 0.00 3.71
7 8 4.125703 CACCTATCCTGCACAGATTTCTC 58.874 47.826 0.00 0.00 0.00 2.87
8 9 3.521126 ACACCTATCCTGCACAGATTTCT 59.479 43.478 0.00 0.00 0.00 2.52
9 10 3.624861 CACACCTATCCTGCACAGATTTC 59.375 47.826 0.00 0.00 0.00 2.17
10 11 3.009473 ACACACCTATCCTGCACAGATTT 59.991 43.478 0.00 0.00 0.00 2.17
11 12 2.573462 ACACACCTATCCTGCACAGATT 59.427 45.455 0.00 0.00 0.00 2.40
12 13 2.093288 CACACACCTATCCTGCACAGAT 60.093 50.000 0.00 0.46 0.00 2.90
13 14 1.276138 CACACACCTATCCTGCACAGA 59.724 52.381 0.00 0.00 0.00 3.41
14 15 1.276138 TCACACACCTATCCTGCACAG 59.724 52.381 0.00 0.00 0.00 3.66
15 16 1.347062 TCACACACCTATCCTGCACA 58.653 50.000 0.00 0.00 0.00 4.57
16 17 2.679837 CAATCACACACCTATCCTGCAC 59.320 50.000 0.00 0.00 0.00 4.57
17 18 2.356022 CCAATCACACACCTATCCTGCA 60.356 50.000 0.00 0.00 0.00 4.41
18 19 2.292267 CCAATCACACACCTATCCTGC 58.708 52.381 0.00 0.00 0.00 4.85
19 20 3.273434 CACCAATCACACACCTATCCTG 58.727 50.000 0.00 0.00 0.00 3.86
20 21 2.912956 ACACCAATCACACACCTATCCT 59.087 45.455 0.00 0.00 0.00 3.24
21 22 3.055094 AGACACCAATCACACACCTATCC 60.055 47.826 0.00 0.00 0.00 2.59
22 23 4.081420 AGAGACACCAATCACACACCTATC 60.081 45.833 0.00 0.00 0.00 2.08
23 24 3.840666 AGAGACACCAATCACACACCTAT 59.159 43.478 0.00 0.00 0.00 2.57
24 25 3.006859 CAGAGACACCAATCACACACCTA 59.993 47.826 0.00 0.00 0.00 3.08
25 26 2.050144 AGAGACACCAATCACACACCT 58.950 47.619 0.00 0.00 0.00 4.00
26 27 2.146342 CAGAGACACCAATCACACACC 58.854 52.381 0.00 0.00 0.00 4.16
27 28 2.802816 GACAGAGACACCAATCACACAC 59.197 50.000 0.00 0.00 0.00 3.82
28 29 2.433970 TGACAGAGACACCAATCACACA 59.566 45.455 0.00 0.00 0.00 3.72
29 30 3.062763 CTGACAGAGACACCAATCACAC 58.937 50.000 0.00 0.00 0.00 3.82
30 31 2.037641 CCTGACAGAGACACCAATCACA 59.962 50.000 3.32 0.00 0.00 3.58
31 32 2.037772 ACCTGACAGAGACACCAATCAC 59.962 50.000 3.32 0.00 0.00 3.06
32 33 2.329267 ACCTGACAGAGACACCAATCA 58.671 47.619 3.32 0.00 0.00 2.57
33 34 3.070018 CAACCTGACAGAGACACCAATC 58.930 50.000 3.32 0.00 0.00 2.67
34 35 2.439507 ACAACCTGACAGAGACACCAAT 59.560 45.455 3.32 0.00 0.00 3.16
35 36 1.837439 ACAACCTGACAGAGACACCAA 59.163 47.619 3.32 0.00 0.00 3.67
36 37 1.496060 ACAACCTGACAGAGACACCA 58.504 50.000 3.32 0.00 0.00 4.17
37 38 2.213499 CAACAACCTGACAGAGACACC 58.787 52.381 3.32 0.00 0.00 4.16
38 39 2.906354 ACAACAACCTGACAGAGACAC 58.094 47.619 3.32 0.00 0.00 3.67
39 40 3.055458 TGAACAACAACCTGACAGAGACA 60.055 43.478 3.32 0.00 0.00 3.41
40 41 3.531538 TGAACAACAACCTGACAGAGAC 58.468 45.455 3.32 0.00 0.00 3.36
41 42 3.904800 TGAACAACAACCTGACAGAGA 57.095 42.857 3.32 0.00 0.00 3.10
42 43 3.251729 CCATGAACAACAACCTGACAGAG 59.748 47.826 3.32 0.00 0.00 3.35
43 44 3.213506 CCATGAACAACAACCTGACAGA 58.786 45.455 3.32 0.00 0.00 3.41
44 45 2.287788 GCCATGAACAACAACCTGACAG 60.288 50.000 0.00 0.00 0.00 3.51
45 46 1.680735 GCCATGAACAACAACCTGACA 59.319 47.619 0.00 0.00 0.00 3.58
46 47 1.000274 GGCCATGAACAACAACCTGAC 60.000 52.381 0.00 0.00 0.00 3.51
47 48 1.133513 AGGCCATGAACAACAACCTGA 60.134 47.619 5.01 0.00 31.98 3.86
48 49 1.270550 GAGGCCATGAACAACAACCTG 59.729 52.381 5.01 0.00 32.88 4.00
49 50 1.133513 TGAGGCCATGAACAACAACCT 60.134 47.619 5.01 0.00 34.55 3.50
50 51 1.327303 TGAGGCCATGAACAACAACC 58.673 50.000 5.01 0.00 0.00 3.77
51 52 3.005684 TGAATGAGGCCATGAACAACAAC 59.994 43.478 5.01 0.00 32.36 3.32
52 53 3.229293 TGAATGAGGCCATGAACAACAA 58.771 40.909 5.01 0.00 32.36 2.83
53 54 2.874014 TGAATGAGGCCATGAACAACA 58.126 42.857 5.01 0.17 32.36 3.33
54 55 3.444742 TGATGAATGAGGCCATGAACAAC 59.555 43.478 5.01 0.00 32.36 3.32
55 56 3.699413 TGATGAATGAGGCCATGAACAA 58.301 40.909 5.01 0.00 32.36 2.83
56 57 3.369242 TGATGAATGAGGCCATGAACA 57.631 42.857 5.01 0.00 32.36 3.18
57 58 3.005472 CCATGATGAATGAGGCCATGAAC 59.995 47.826 5.01 0.00 38.72 3.18
58 59 3.117436 TCCATGATGAATGAGGCCATGAA 60.117 43.478 5.01 0.00 38.72 2.57
59 60 2.444010 TCCATGATGAATGAGGCCATGA 59.556 45.455 5.01 0.00 38.72 3.07
60 61 2.871453 TCCATGATGAATGAGGCCATG 58.129 47.619 5.01 0.00 38.72 3.66
61 62 3.827817 ATCCATGATGAATGAGGCCAT 57.172 42.857 5.01 0.00 38.72 4.40
62 63 3.117436 TCAATCCATGATGAATGAGGCCA 60.117 43.478 5.01 0.00 38.72 5.36
63 64 3.493334 TCAATCCATGATGAATGAGGCC 58.507 45.455 0.00 0.00 38.72 5.19
64 65 4.022242 CCTTCAATCCATGATGAATGAGGC 60.022 45.833 0.00 0.00 38.72 4.70
65 66 5.241064 GTCCTTCAATCCATGATGAATGAGG 59.759 44.000 0.00 0.69 38.72 3.86
66 67 5.826208 TGTCCTTCAATCCATGATGAATGAG 59.174 40.000 0.00 0.00 38.72 2.90
67 68 5.757988 TGTCCTTCAATCCATGATGAATGA 58.242 37.500 0.00 2.41 38.72 2.57
68 69 6.264518 TGATGTCCTTCAATCCATGATGAATG 59.735 38.462 0.00 0.02 38.03 2.67
69 70 6.370453 TGATGTCCTTCAATCCATGATGAAT 58.630 36.000 0.00 0.00 38.03 2.57
70 71 5.757988 TGATGTCCTTCAATCCATGATGAA 58.242 37.500 0.00 1.35 38.03 2.57
71 72 5.376756 TGATGTCCTTCAATCCATGATGA 57.623 39.130 0.00 0.00 38.03 2.92
72 73 6.650427 ATTGATGTCCTTCAATCCATGATG 57.350 37.500 0.00 0.00 41.37 3.07
73 74 7.781219 TGTTATTGATGTCCTTCAATCCATGAT 59.219 33.333 10.59 0.00 43.50 2.45
74 75 7.118060 TGTTATTGATGTCCTTCAATCCATGA 58.882 34.615 10.59 0.00 43.50 3.07
75 76 7.337480 TGTTATTGATGTCCTTCAATCCATG 57.663 36.000 10.59 0.00 43.50 3.66
76 77 7.959658 TTGTTATTGATGTCCTTCAATCCAT 57.040 32.000 10.59 0.00 43.50 3.41
77 78 7.614974 TGATTGTTATTGATGTCCTTCAATCCA 59.385 33.333 10.59 7.48 43.50 3.41
78 79 7.917505 GTGATTGTTATTGATGTCCTTCAATCC 59.082 37.037 10.59 5.58 43.50 3.01
79 80 8.461222 TGTGATTGTTATTGATGTCCTTCAATC 58.539 33.333 10.59 0.00 43.50 2.67
80 81 8.352137 TGTGATTGTTATTGATGTCCTTCAAT 57.648 30.769 11.63 11.63 45.74 2.57
81 82 7.757941 TGTGATTGTTATTGATGTCCTTCAA 57.242 32.000 0.00 0.00 39.77 2.69
82 83 7.757941 TTGTGATTGTTATTGATGTCCTTCA 57.242 32.000 0.00 0.00 0.00 3.02
91 92 9.707957 ACCCCTTATATTTGTGATTGTTATTGA 57.292 29.630 0.00 0.00 0.00 2.57
92 93 9.748708 CACCCCTTATATTTGTGATTGTTATTG 57.251 33.333 0.00 0.00 0.00 1.90
93 94 9.707957 TCACCCCTTATATTTGTGATTGTTATT 57.292 29.630 0.00 0.00 31.45 1.40
94 95 9.881773 ATCACCCCTTATATTTGTGATTGTTAT 57.118 29.630 0.00 0.00 42.36 1.89
96 97 9.354673 CTATCACCCCTTATATTTGTGATTGTT 57.645 33.333 8.53 0.00 42.36 2.83
97 98 8.723365 TCTATCACCCCTTATATTTGTGATTGT 58.277 33.333 8.53 0.00 42.36 2.71
98 99 9.224267 CTCTATCACCCCTTATATTTGTGATTG 57.776 37.037 8.53 7.25 42.36 2.67
99 100 8.386264 CCTCTATCACCCCTTATATTTGTGATT 58.614 37.037 8.53 0.00 42.36 2.57
100 101 7.037297 CCCTCTATCACCCCTTATATTTGTGAT 60.037 40.741 8.32 8.32 45.68 3.06
101 102 6.272324 CCCTCTATCACCCCTTATATTTGTGA 59.728 42.308 0.00 0.00 39.95 3.58
102 103 6.044404 ACCCTCTATCACCCCTTATATTTGTG 59.956 42.308 0.00 0.00 0.00 3.33
103 104 6.158260 ACCCTCTATCACCCCTTATATTTGT 58.842 40.000 0.00 0.00 0.00 2.83
104 105 6.272324 TGACCCTCTATCACCCCTTATATTTG 59.728 42.308 0.00 0.00 0.00 2.32
105 106 6.399013 TGACCCTCTATCACCCCTTATATTT 58.601 40.000 0.00 0.00 0.00 1.40
106 107 5.989717 TGACCCTCTATCACCCCTTATATT 58.010 41.667 0.00 0.00 0.00 1.28
107 108 5.633473 TGACCCTCTATCACCCCTTATAT 57.367 43.478 0.00 0.00 0.00 0.86
108 109 5.403512 CTTGACCCTCTATCACCCCTTATA 58.596 45.833 0.00 0.00 0.00 0.98
109 110 4.235372 CTTGACCCTCTATCACCCCTTAT 58.765 47.826 0.00 0.00 0.00 1.73
110 111 3.632645 CCTTGACCCTCTATCACCCCTTA 60.633 52.174 0.00 0.00 0.00 2.69
111 112 2.482494 CTTGACCCTCTATCACCCCTT 58.518 52.381 0.00 0.00 0.00 3.95
112 113 1.344496 CCTTGACCCTCTATCACCCCT 60.344 57.143 0.00 0.00 0.00 4.79
113 114 1.132500 CCTTGACCCTCTATCACCCC 58.868 60.000 0.00 0.00 0.00 4.95
114 115 1.132500 CCCTTGACCCTCTATCACCC 58.868 60.000 0.00 0.00 0.00 4.61
115 116 0.470341 GCCCTTGACCCTCTATCACC 59.530 60.000 0.00 0.00 0.00 4.02
116 117 0.470341 GGCCCTTGACCCTCTATCAC 59.530 60.000 0.00 0.00 0.00 3.06
117 118 0.044092 TGGCCCTTGACCCTCTATCA 59.956 55.000 0.00 0.00 0.00 2.15
118 119 0.470341 GTGGCCCTTGACCCTCTATC 59.530 60.000 0.00 0.00 0.00 2.08
119 120 0.253160 TGTGGCCCTTGACCCTCTAT 60.253 55.000 0.00 0.00 0.00 1.98
120 121 0.253160 ATGTGGCCCTTGACCCTCTA 60.253 55.000 0.00 0.00 0.00 2.43
121 122 1.542375 ATGTGGCCCTTGACCCTCT 60.542 57.895 0.00 0.00 0.00 3.69
122 123 1.379044 CATGTGGCCCTTGACCCTC 60.379 63.158 0.00 0.00 0.00 4.30
123 124 2.765969 CATGTGGCCCTTGACCCT 59.234 61.111 0.00 0.00 0.00 4.34
124 125 3.070576 GCATGTGGCCCTTGACCC 61.071 66.667 0.00 0.00 36.11 4.46
125 126 3.443045 CGCATGTGGCCCTTGACC 61.443 66.667 0.00 0.00 40.31 4.02
126 127 2.672996 ACGCATGTGGCCCTTGAC 60.673 61.111 11.65 0.00 40.31 3.18
127 128 2.672651 CACGCATGTGGCCCTTGA 60.673 61.111 11.65 0.00 42.59 3.02
128 129 4.424566 GCACGCATGTGGCCCTTG 62.425 66.667 11.65 1.32 46.51 3.61
134 135 4.720902 TGGAGGGCACGCATGTGG 62.721 66.667 11.65 0.76 46.51 4.17
136 137 4.415150 CCTGGAGGGCACGCATGT 62.415 66.667 0.00 0.00 0.00 3.21
173 174 5.874261 CCCAAACAGACAACAAAAATGTTCT 59.126 36.000 0.00 0.00 33.17 3.01
174 175 5.447144 GCCCAAACAGACAACAAAAATGTTC 60.447 40.000 0.00 0.00 33.17 3.18
179 181 3.594134 CAGCCCAAACAGACAACAAAAA 58.406 40.909 0.00 0.00 0.00 1.94
184 186 1.109323 AGCCAGCCCAAACAGACAAC 61.109 55.000 0.00 0.00 0.00 3.32
185 187 1.108727 CAGCCAGCCCAAACAGACAA 61.109 55.000 0.00 0.00 0.00 3.18
186 188 1.529010 CAGCCAGCCCAAACAGACA 60.529 57.895 0.00 0.00 0.00 3.41
190 192 2.132996 CAACCAGCCAGCCCAAACA 61.133 57.895 0.00 0.00 0.00 2.83
198 200 2.270986 GGCAACTCCAACCAGCCAG 61.271 63.158 0.00 0.00 44.59 4.85
201 203 0.251165 TTAGGGCAACTCCAACCAGC 60.251 55.000 0.00 0.00 36.21 4.85
203 205 1.707989 TGATTAGGGCAACTCCAACCA 59.292 47.619 0.00 0.00 36.21 3.67
221 223 6.607198 AGACAATGAAGGGTTTCTTTTCTTGA 59.393 34.615 0.00 0.00 35.50 3.02
236 238 2.966708 CGACGCAACAAAGACAATGAAG 59.033 45.455 0.00 0.00 0.00 3.02
246 248 2.419324 ACAAAGGTAACGACGCAACAAA 59.581 40.909 0.00 0.00 46.39 2.83
309 311 8.044060 TCTAAAATCCATGACACTTTGATCAC 57.956 34.615 0.00 0.00 0.00 3.06
366 368 1.831106 GATCCCCAAACCCATCCAAAC 59.169 52.381 0.00 0.00 0.00 2.93
422 424 4.709397 TGCATTAGAATTCCCGGTTTGAAT 59.291 37.500 0.00 0.00 33.97 2.57
423 425 4.082845 TGCATTAGAATTCCCGGTTTGAA 58.917 39.130 0.00 0.00 0.00 2.69
426 428 5.418676 CAATTGCATTAGAATTCCCGGTTT 58.581 37.500 0.00 0.00 0.00 3.27
455 941 7.112779 AGAAGGACTTGGTTATCAATACAAGG 58.887 38.462 0.00 0.00 43.36 3.61
457 943 8.044908 GGTAGAAGGACTTGGTTATCAATACAA 58.955 37.037 0.00 0.00 34.45 2.41
462 948 5.570844 GCTGGTAGAAGGACTTGGTTATCAA 60.571 44.000 0.00 0.00 0.00 2.57
467 953 2.039084 CTGCTGGTAGAAGGACTTGGTT 59.961 50.000 0.00 0.00 0.00 3.67
491 1142 1.134965 GGTCATGCTAGTCGTTGCTCT 60.135 52.381 0.00 0.00 0.00 4.09
508 1159 3.018423 ACCATTGGCTAGGATTTGGTC 57.982 47.619 1.54 0.00 32.08 4.02
551 1202 1.981256 ACGGTGGCAACTGAGAAATT 58.019 45.000 7.18 0.00 36.45 1.82
559 1218 4.811206 TTGCATACGGTGGCAACT 57.189 50.000 15.18 0.00 44.41 3.16
593 1252 3.181484 CGTGTATGTACCCGAGGAAATCA 60.181 47.826 0.00 0.00 0.00 2.57
600 1259 3.120792 CAATTCCGTGTATGTACCCGAG 58.879 50.000 0.00 0.00 0.00 4.63
623 1282 3.920412 TTCAATCATGAGAACGACAGACG 59.080 43.478 0.09 0.00 41.55 4.18
627 1289 5.048852 TGCATTTTCAATCATGAGAACGACA 60.049 36.000 0.09 0.00 36.78 4.35
631 1293 5.220154 CGCTTGCATTTTCAATCATGAGAAC 60.220 40.000 0.09 0.00 36.78 3.01
648 1314 0.814457 AAAGTTCCAACACGCTTGCA 59.186 45.000 0.00 0.00 0.00 4.08
677 1343 0.591170 CGTGGAAATGTCAAAGCCGT 59.409 50.000 0.00 0.00 0.00 5.68
712 1378 3.640029 TGGTCAGTCTACGTCTTCCTTTT 59.360 43.478 0.00 0.00 0.00 2.27
716 1382 3.870633 ATTGGTCAGTCTACGTCTTCC 57.129 47.619 0.00 0.00 0.00 3.46
748 1414 6.754702 TTGAGACCGTAGATATACCATAGC 57.245 41.667 0.00 0.00 0.00 2.97
751 1417 7.834881 TTCTTTGAGACCGTAGATATACCAT 57.165 36.000 0.00 0.00 0.00 3.55
759 1425 5.862323 CGAAAGAATTCTTTGAGACCGTAGA 59.138 40.000 32.67 0.00 45.37 2.59
767 1433 5.931441 ACTGGTCGAAAGAATTCTTTGAG 57.069 39.130 32.67 25.15 45.37 3.02
768 1434 5.408604 GCTACTGGTCGAAAGAATTCTTTGA 59.591 40.000 32.67 25.34 45.37 2.69
772 1438 4.499183 CTGCTACTGGTCGAAAGAATTCT 58.501 43.478 0.88 0.88 45.01 2.40
796 1462 8.258708 ACTAGATGTGTTTAATCTAACCACTCC 58.741 37.037 0.00 0.00 36.46 3.85
799 1465 9.530633 CCTACTAGATGTGTTTAATCTAACCAC 57.469 37.037 0.00 0.00 36.46 4.16
836 1502 2.896168 TGGGAATTGGTCGTAATCGTC 58.104 47.619 0.00 0.00 38.33 4.20
841 1507 2.953284 TGGTTGGGAATTGGTCGTAA 57.047 45.000 0.00 0.00 0.00 3.18
976 1644 3.445450 GTGTGAGCTAGTCTTGGATCTGA 59.555 47.826 0.00 0.00 0.00 3.27
988 1657 3.449018 ACCTTAGACATGGTGTGAGCTAG 59.551 47.826 0.00 0.00 34.90 3.42
1018 1697 4.026475 CGAAGCAGAACGAAGAATATGGTC 60.026 45.833 0.00 0.00 0.00 4.02
1041 1720 1.544691 TCTACACCCTCGAAAGACAGC 59.455 52.381 0.00 0.00 35.39 4.40
1043 1722 2.589720 TGTCTACACCCTCGAAAGACA 58.410 47.619 0.00 0.00 43.08 3.41
1047 1726 1.066430 GGCATGTCTACACCCTCGAAA 60.066 52.381 0.00 0.00 0.00 3.46
1071 1750 8.443160 CAGTACTACAAATGTTTTCATGATCGT 58.557 33.333 0.00 0.00 40.79 3.73
1089 1768 9.893305 AAAACACAAGCATAAATTCAGTACTAC 57.107 29.630 0.00 0.00 0.00 2.73
1091 1770 7.803189 CGAAAACACAAGCATAAATTCAGTACT 59.197 33.333 0.00 0.00 0.00 2.73
1101 1780 3.971871 CGAAAGCGAAAACACAAGCATAA 59.028 39.130 0.00 0.00 40.82 1.90
1117 1796 1.138247 CTGCAGGCCATTCGAAAGC 59.862 57.895 5.01 13.56 0.00 3.51
1238 1948 0.320771 GCGGTGCAGGATATACAGGG 60.321 60.000 0.00 0.00 0.00 4.45
1256 1966 1.129437 CGGTAAAGAGAAGCAGCAAGC 59.871 52.381 0.00 0.00 46.19 4.01
1321 2033 2.546321 GTCAGCGTGCACTTGTCG 59.454 61.111 16.19 1.75 0.00 4.35
1654 2415 2.124193 TAGCCGTAGCCGTAGCCA 60.124 61.111 0.00 0.00 41.25 4.75
1825 2599 4.634443 ACAAAGCATATGAACTACGGAACC 59.366 41.667 6.97 0.00 0.00 3.62
1828 2602 4.827692 ACACAAAGCATATGAACTACGGA 58.172 39.130 6.97 0.00 0.00 4.69
1855 2629 0.179103 AACTGCAGCAAGCCAACAAC 60.179 50.000 15.27 0.00 44.83 3.32
1887 2661 1.141053 AGTAACCAGGGAATCATCGCC 59.859 52.381 0.00 0.00 39.23 5.54
1937 2711 8.696410 TTTCACTTTGTTTATGAGAAACAACC 57.304 30.769 16.62 0.00 46.14 3.77
1979 2757 9.549509 CAATTTCTTCGGTTCGTTTTCATATAA 57.450 29.630 0.00 0.00 0.00 0.98
1980 2758 8.178964 CCAATTTCTTCGGTTCGTTTTCATATA 58.821 33.333 0.00 0.00 0.00 0.86
1986 2764 4.096682 TGACCAATTTCTTCGGTTCGTTTT 59.903 37.500 0.00 0.00 31.63 2.43
2035 2813 0.100861 GCTGGCGACCTAGTAGTGTC 59.899 60.000 8.11 8.11 0.00 3.67
2038 2816 1.757340 GGGCTGGCGACCTAGTAGT 60.757 63.158 0.00 0.00 34.48 2.73
2154 2933 1.890489 TGCATGCCCAATGATAGCATC 59.110 47.619 16.68 0.00 45.16 3.91
2167 2946 1.538047 TTCTTCAAGTCCTGCATGCC 58.462 50.000 16.68 0.00 0.00 4.40
2205 2984 6.258068 GCTAAATTATTGGCCTAGGTATAGCG 59.742 42.308 11.31 0.00 37.08 4.26
2206 2985 7.281100 CAGCTAAATTATTGGCCTAGGTATAGC 59.719 40.741 11.31 10.20 43.48 2.97
2250 3029 2.811431 GACAACACATGACCCGATCAAA 59.189 45.455 0.00 0.00 41.93 2.69
2256 3035 0.034756 TCAGGACAACACATGACCCG 59.965 55.000 0.00 0.00 43.87 5.28
2258 3037 3.058016 CACATTCAGGACAACACATGACC 60.058 47.826 0.00 0.00 43.25 4.02
2279 3058 3.425659 CGACAGATGATATCCCTCCTCA 58.574 50.000 0.00 0.00 0.00 3.86
2300 3079 5.238583 TCTCTAGCAAAAGCTTGAAGTACC 58.761 41.667 0.00 0.00 34.14 3.34
2329 3108 3.791320 AGGGATAGAGAAGTGTGGTCAA 58.209 45.455 0.00 0.00 0.00 3.18
2340 3119 3.269643 TCTCCAGTGTCAAGGGATAGAGA 59.730 47.826 0.00 0.00 0.00 3.10
2380 3159 4.287067 AGCACCCAAGAGTTCTCAAATCTA 59.713 41.667 2.64 0.00 0.00 1.98
2404 3183 7.693969 CAGAAATTCTGTAAATCCCTCTGTT 57.306 36.000 14.47 0.00 39.58 3.16
2506 3285 7.336931 TCTGCATTTTTATTCCACTCTCTAACC 59.663 37.037 0.00 0.00 0.00 2.85
2514 3293 5.927281 AGCATCTGCATTTTTATTCCACT 57.073 34.783 4.79 0.00 45.16 4.00
2531 3310 9.860898 AATCTTAATTTTTCTGTACCAAGCATC 57.139 29.630 0.00 0.00 0.00 3.91
2639 3418 4.254492 GGCCAATCGTTCTCTTAAGTCTT 58.746 43.478 0.00 0.00 0.00 3.01
2640 3419 3.260884 TGGCCAATCGTTCTCTTAAGTCT 59.739 43.478 0.61 0.00 0.00 3.24
2666 3445 9.868389 GCCATTTCATTTCTTCTTGTTTTAAAG 57.132 29.630 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.