Locus 2247

Sequence ID	X_DroMel_CAF1
Location	6,065,082 – 6,065,267
Length	185
Max. P	0.932897

overview

Window 8

Location	6,065,082 – 6,065,187
Length	105
Sequences	4
Columns	105
Reading direction	forward
Mean pairwise identity	80.10
Mean single sequence MFE	-23.93
Consensus MFE	-17.50
Energy contribution	-18.75
Covariance contribution	1.25
Combinations/Pair	1.17
Mean z-score	-1.67
Structure conservation index	0.73
SVM decision value	0.35
SVM RNA-class probability	0.702121
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6065082 105 + 22224390
UCUCGAUAAUUGUUGCACGCGAUAUCGAUUGUCGCCCCAAACUUAAAGCUCUGCCCGAACUAACAGCUUUUUUCGACCAACCACCAAUAGCUGGUCACACCAGCA
..((((.((..((((...((((((.....))))))...........((.((.....)).))..))))..)).)))).............(((((.....))))). ( -24.10)
>DroSec_CAF1 76007 94 + 1
UGGCGAUAAUUGUUGCAAUCGAUAUCGAUUGUCGCCCCGAACUUAAAGCUCUGC---AACUUACGGCUUUUCCCGAC-------CACUAGCUGGUCACACCGGC-
.(((((((((((...(....)....)))))))))))(((.....((((((.((.---....)).))))))....(((-------((.....)))))....))).- ( -27.30)
>DroSim_CAF1 72108 102 + 1
UGGCGAUAAUUGUUGCAAUCGAUAUCGAUUGUCGCCCCGAACUUAAAGCUCUGC---AACUUACGCCUUUUCCCGACCAACCACCACUAGCUGGUCACACCAGCA
.((((.(((..((((((((((....))))).(((...)))............))---))))))))))......................(((((.....))))). ( -25.80)
>DroYak_CAF1 76471 98 + 1
UGGCGAUUAUUGUUACCAGCGAAUUCGAUUGUCGCCAAUAACUUAAAGCUCUCC---AACUGACGGCAUUUUCCGAUU---CACCACAACCUGGUCACACU-GCG
(((((((.((((.............)))).)))))))..........((.....---......(((......)))...---.((((.....))))......-)). ( -18.52)
>consensus
UGGCGAUAAUUGUUGCAAGCGAUAUCGAUUGUCGCCCCGAACUUAAAGCUCUGC___AACUUACGGCUUUUCCCGACC___CACCACUAGCUGGUCACACCAGCA
.(((((((((((.............)))))))))))........((((((.((........)).))))))...................(((((.....))))). (-17.50 = -18.75 +   1.25)

alignment

secondary structure

dotplot

Window 9

Location	6,065,107 – 6,065,227
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	83.19
Mean single sequence MFE	-28.40
Consensus MFE	-21.04
Energy contribution	-21.85
Covariance contribution	0.81
Combinations/Pair	1.13
Mean z-score	-2.19
Structure conservation index	0.74
SVM decision value	1.22
SVM RNA-class probability	0.932897
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6065107 120 + 22224390
CGAUUGUCGCCCCAAACUUAAAGCUCUGCCCGAACUAACAGCUUUUUUCGACCAACCACCAAUAGCUGGUCACACCAGCAGCAGCAAUCUUCAGCUGUUCAACAACAACAGCACGCGGCA
....((((((............(((((((..(((..((....))..)))(((((.(........).)))))......)))).)))........((((((.......))))))..)))))) ( -30.40)
>DroSec_CAF1 76032 107 + 1
CGAUUGUCGCCCCGAACUUAAAGCUCUGC---AACUUACGGCUUUUCCCGAC-------CACUAGCUGGUCACACCGGC---AGCAGUCUUCAGCUGUUCAACAACAACAGCACGCGGCA
....((((((..........(((..((((---......(((......)))..-------.....(((((.....)))))---.)))).)))..((((((.......))))))..)))))) ( -32.40)
>DroSim_CAF1 72133 117 + 1
CGAUUGUCGCCCCGAACUUAAAGCUCUGC---AACUUACGCCUUUUCCCGACCAACCACCACUAGCUGGUCACACCAGCAGCAGCAGUCUUCAGCUGUUCAACAACAACAGCACGCGGCA
....((((((..........(((((((((---......((........))..............(((((.....))))).)))).)).)))..((((((.......))))))..)))))) ( -31.20)
>DroYak_CAF1 76496 113 + 1
CGAUUGUCGCCAAUAACUUAAAGCUCUCC---AACUGACGGCAUUUUCCGAUU---CACCACAACCUGGUCACACU-GCGCCAGCGAACUUCAGCUGUUCCACAACAACAACACGCGGCA
....((((((............((.....---......(((......)))...---.((((.....))))......-))..((((........)))).................)))))) ( -19.60)
>consensus
CGAUUGUCGCCCCGAACUUAAAGCUCUGC___AACUUACGGCUUUUCCCGACC___CACCACUAGCUGGUCACACCAGCAGCAGCAAUCUUCAGCUGUUCAACAACAACAGCACGCGGCA
....((((((............(((.............(((......)))..............(((((.....)))))...)))........((((((.......))))))..)))))) (-21.04 = -21.85 +   0.81)

alignment

secondary structure

dotplot

Window 0

Location	6,065,147 – 6,065,267
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	85.36
Mean single sequence MFE	-24.96
Consensus MFE	-17.05
Energy contribution	-17.30
Covariance contribution	0.25
Combinations/Pair	1.17
Mean z-score	-1.88
Structure conservation index	0.68
SVM decision value	0.43
SVM RNA-class probability	0.735277
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6065147 120 + 22224390
GCUUUUUUCGACCAACCACCAAUAGCUGGUCACACCAGCAGCAGCAAUCUUCAGCUGUUCAACAACAACAGCACGCGGCAGCAACUACAACAAAACAUUAAGAUUGUAAUCAAGUUGUUA
............((((........(((((.....)))))....((((((((..((((((.......))))))..((....)).................))))))))......))))... ( -28.10)
>DroSec_CAF1 76069 110 + 1
GCUUUUCCCGAC-------CACUAGCUGGUCACACCGGC---AGCAGUCUUCAGCUGUUCAACAACAACAGCACGCGGCAGAAACUACAACAAUACAUUAAGAUUGUAAUCAAGCUGUUA
((.......(((-------..((.(((((.....)))))---))..)))....((((((.......))))))..))(((((........(((((........))))).......))))). ( -26.76)
>DroSim_CAF1 72170 120 + 1
CCUUUUCCCGACCAACCACCACUAGCUGGUCACACCAGCAGCAGCAGUCUUCAGCUGUUCAACAACAACAGCACGCGGCAGAAACUACAACAAAACAUUAAGAUUGUAAUCAAGCUGUUA
........................(((((.....)))))((((((.(((....((((((.......))))))....)))......((((((..........).))))).....)))))). ( -26.40)
>DroYak_CAF1 76533 116 + 1
GCAUUUUCCGAUU---CACCACAACCUGGUCACACU-GCGCCAGCGAACUUCAGCUGUUCCACAACAACAACACGCGGCAGCGACUACAACAAAACAAUAAGAUUGUAAUCAAGUUGUUA
.............---.........(((((......-..))))).((((.......))))......((((((..((....))((.((((((..........).))))).))..)))))). ( -18.60)
>consensus
GCUUUUCCCGACC___CACCACUAGCUGGUCACACCAGCAGCAGCAAUCUUCAGCUGUUCAACAACAACAGCACGCGGCAGAAACUACAACAAAACAUUAAGAUUGUAAUCAAGCUGUUA
.........((.............(((((.....)))))....((((((((..((((((.......))))))..(..(......)..)...........))))))))..))......... (-17.05 = -17.30 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:41 2006