Locus 1058

Sequence ID	2L_DroMel_CAF1
Location	2,938,783 – 2,938,983
Length	200
Max. P	0.994799

overview

Window 6

Location	2,938,783 – 2,938,903
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.83
Mean single sequence MFE	-22.50
Consensus MFE	-21.81
Energy contribution	-21.57
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-1.28
Structure conservation index	0.97
SVM decision value	0.33
SVM RNA-class probability	0.690066
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2938783 120 + 22407834
GCCGGUUUUGUACUUCUUGCAACAAUGCAAUUUCAAUUUAAACUGUUAUUAUUUUGUACAUUUCACUUGAACAAUUUCUGUGAUUUGUUUUUGUUUUAGCCGGCACAGCUGUGCCCGCCC
..((((((........(((((....))))).........))))))............(((..((((..(((....))).))))..)))..........((.(((((....))))).)).. ( -25.43)
>DroSec_CAF1 53824 120 + 1
GCCGGUUUUGUACUUCUUGCAACAAUGCAAUUUCAAUUUAAACUGUUAUUAUUUUGUACAUUUCACUUGAACAAUUUCUCUGAUUUGUUUUUGUUUUAGCCGGCACAGCUGUGCCCGCCC
..((((((........(((((....))))).........))))))...................((..((((((..........))))))..))....((.(((((....))))).)).. ( -22.33)
>DroSim_CAF1 55862 120 + 1
GCCGGUUUUGUACUUCUUGCAACAAUGCAAUUUCAAUUUAAACUGUUAUUAUUUUGUACAUUUCACUUGAACAAUUUCUCUGAUUUGUUUUUGUUUUAGCCGGCACAGCUGUGCCCGCCC
..((((((........(((((....))))).........))))))...................((..((((((..........))))))..))....((.(((((....))))).)).. ( -22.33)
>DroEre_CAF1 56142 120 + 1
ACCGGUUUUGUACUUCUUGCAACAAUGCAAUUUCAAUUUAAACUGUUAUUAUUUUGUACAUUUCACUUGAACAAUUUCUCUGAUUUGUUUUUGUUUUAGCCGGCACAGCUGUGCUCGCCC
..((((((........(((((....))))).........))))))...................((..((((((..........))))))..))....((.(((((....))))).)).. ( -20.43)
>DroYak_CAF1 56041 120 + 1
GCCGGUUUUGUACUUCUUGCAACAAUGCAAUUUCAAUUUAAACUGUUAUUAUUUUGUACAUUUCACUUGAACAAUUUCUCUGAUUUGUUUUUGUUUUAGCCGGCACAGCUGUGCUCGCCC
(((((((.(((((.....(((....)))(((..((........))..))).....)))))....((..((((((..........))))))..))...)))))))................ ( -22.00)
>consensus
GCCGGUUUUGUACUUCUUGCAACAAUGCAAUUUCAAUUUAAACUGUUAUUAUUUUGUACAUUUCACUUGAACAAUUUCUCUGAUUUGUUUUUGUUUUAGCCGGCACAGCUGUGCCCGCCC
..((((((........(((((....))))).........))))))...................((..((((((..........))))))..))....((.(((((....))))).)).. (-21.81 = -21.57 +  -0.24)

alignment

secondary structure

dotplot

Window 7

Location	2,938,783 – 2,938,903
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.83
Mean single sequence MFE	-25.00
Consensus MFE	-23.38
Energy contribution	-23.78
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.87
Structure conservation index	0.94
SVM decision value	1.85
SVM RNA-class probability	0.979996
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2938783 120 - 22407834
GGGCGGGCACAGCUGUGCCGGCUAAAACAAAAACAAAUCACAGAAAUUGUUCAAGUGAAAUGUACAAAAUAAUAACAGUUUAAAUUGAAAUUGCAUUGUUGCAAGAAGUACAAAACCGGC
((((.(((((....))))).))...............((((.(((....)))..))))..(((((..........((((....))))...(((((....)))))...)))))...))... ( -28.60)
>DroSec_CAF1 53824 120 - 1
GGGCGGGCACAGCUGUGCCGGCUAAAACAAAAACAAAUCAGAGAAAUUGUUCAAGUGAAAUGUACAAAAUAAUAACAGUUUAAAUUGAAAUUGCAUUGUUGCAAGAAGUACAAAACCGGC
((((.(((((....))))).))......................................(((((..........((((....))))...(((((....)))))...)))))...))... ( -26.10)
>DroSim_CAF1 55862 120 - 1
GGGCGGGCACAGCUGUGCCGGCUAAAACAAAAACAAAUCAGAGAAAUUGUUCAAGUGAAAUGUACAAAAUAAUAACAGUUUAAAUUGAAAUUGCAUUGUUGCAAGAAGUACAAAACCGGC
((((.(((((....))))).))......................................(((((..........((((....))))...(((((....)))))...)))))...))... ( -26.10)
>DroEre_CAF1 56142 120 - 1
GGGCGAGCACAGCUGUGCCGGCUAAAACAAAAACAAAUCAGAGAAAUUGUUCAAGUGAAAUGUACAAAAUAAUAACAGUUUAAAUUGAAAUUGCAUUGUUGCAAGAAGUACAAAACCGGU
((.((.((((....))))))(((..(((((................)))))..)))....(((((..........((((....))))...(((((....)))))...)))))...))... ( -22.09)
>DroYak_CAF1 56041 120 - 1
GGGCGAGCACAGCUGUGCCGGCUAAAACAAAAACAAAUCAGAGAAAUUGUUCAAGUGAAAUGUACAAAAUAAUAACAGUUUAAAUUGAAAUUGCAUUGUUGCAAGAAGUACAAAACCGGC
.(((.......)))..(((((......((..(((((..........)))))....))...(((((..........((((....))))...(((((....)))))...)))))...))))) ( -22.10)
>consensus
GGGCGGGCACAGCUGUGCCGGCUAAAACAAAAACAAAUCAGAGAAAUUGUUCAAGUGAAAUGUACAAAAUAAUAACAGUUUAAAUUGAAAUUGCAUUGUUGCAAGAAGUACAAAACCGGC
((((.(((((....))))).))......................................(((((..........((((....))))...(((((....)))))...)))))...))... (-23.38 = -23.78 +   0.40)

alignment

secondary structure

dotplot

Window 8

Location	2,938,863 – 2,938,983
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.66
Mean single sequence MFE	-34.06
Consensus MFE	-33.42
Energy contribution	-33.02
Covariance contribution	-0.40
Combinations/Pair	1.07
Mean z-score	-1.22
Structure conservation index	0.98
SVM decision value	0.87
SVM RNA-class probability	0.869842
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2938863 120 + 22407834
UGAUUUGUUUUUGUUUUAGCCGGCACAGCUGUGCCCGCCCGUCGCUCGAAUGGGCAUUAUUGUGAUCCAGUGAACGUGCCGGCUUAUUGGAAAUCGUUCUGACCAUGUAUUGAUGUUUUU
.((...((((..(....(((((((((.....((((((..((.....))..))))))((((((.....))))))..)))))))))...)..))))...))..................... ( -35.50)
>DroSec_CAF1 53904 120 + 1
UGAUUUGUUUUUGUUUUAGCCGGCACAGCUGUGCCCGCCCGUCGCUCGAAUGGGCAUUAUUGUGAUCCAAUGAACGUGCCGGCUUAUUGGAAAUCGUUCUGACCAUGUAUUGAUGCUUUU
.((...((((..(....(((((((((.....((((((..((.....))..))))))((((((.....))))))..)))))))))...)..))))...))..................... ( -35.50)
>DroSim_CAF1 55942 120 + 1
UGAUUUGUUUUUGUUUUAGCCGGCACAGCUGUGCCCGCCCGUCGCUCGAAUGGGCAUUAUUGUGAUCCAAUGAACGUGCCGGCUUAUUGGAAAUCGUUCUGACCAUGUAUUGAUGUUUUU
.((...((((..(....(((((((((.....((((((..((.....))..))))))((((((.....))))))..)))))))))...)..))))...))..................... ( -35.50)
>DroEre_CAF1 56222 118 + 1
UGAUUUGUUUUUGUUUUAGCCGGCACAGCUGUGCUCGCCCGUCGCUUGAAUGGGCAUUAUUGUGAUCCAAUGAACGUGCUGGCUUAUUGGAAAUCGUUCUGACCAUGUAUUGAUAU--UU
.((...((((..(....(((((((((..........((((((.......)))))).((((((.....))))))..)))))))))...)..))))...)).................--.. ( -31.90)
>DroYak_CAF1 56121 118 + 1
UGAUUUGUUUUUGUUUUAGCCGGCACAGCUGUGCUCGCCCGUCGCUUCAAUGGGCAUUAUUGUGAUCCAAUGAACGUGCUGGCUUAUUGGAAAUCGUCCUGACCAUGUAUUGAUAU--UU
.(((..((((..(....(((((((((..........((((((.......)))))).((((((.....))))))..)))))))))...)..)))).)))..................--.. ( -31.90)
>consensus
UGAUUUGUUUUUGUUUUAGCCGGCACAGCUGUGCCCGCCCGUCGCUCGAAUGGGCAUUAUUGUGAUCCAAUGAACGUGCCGGCUUAUUGGAAAUCGUUCUGACCAUGUAUUGAUGUUUUU
.(((((.(....((...(((((((((..........((((((.......)))))).((((((.....))))))..))))))))).)).).)))))......................... (-33.42 = -33.02 +  -0.40)

alignment

secondary structure

dotplot

Window 9

Location	2,938,863 – 2,938,983
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.66
Mean single sequence MFE	-30.08
Consensus MFE	-26.38
Energy contribution	-26.74
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-2.14
Structure conservation index	0.88
SVM decision value	2.51
SVM RNA-class probability	0.994799
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2938863 120 - 22407834
AAAAACAUCAAUACAUGGUCAGAACGAUUUCCAAUAAGCCGGCACGUUCACUGGAUCACAAUAAUGCCCAUUCGAGCGACGGGCGGGCACAGCUGUGCCGGCUAAAACAAAAACAAAUCA
...............(((............)))...(((((((((......((.....))....(((((.((((.....)))).))))).....)))))))))................. ( -31.10)
>DroSec_CAF1 53904 120 - 1
AAAAGCAUCAAUACAUGGUCAGAACGAUUUCCAAUAAGCCGGCACGUUCAUUGGAUCACAAUAAUGCCCAUUCGAGCGACGGGCGGGCACAGCUGUGCCGGCUAAAACAAAAACAAAUCA
...............(((............)))...(((((((((....((((.....))))..(((((.((((.....)))).))))).....)))))))))................. ( -33.20)
>DroSim_CAF1 55942 120 - 1
AAAAACAUCAAUACAUGGUCAGAACGAUUUCCAAUAAGCCGGCACGUUCAUUGGAUCACAAUAAUGCCCAUUCGAGCGACGGGCGGGCACAGCUGUGCCGGCUAAAACAAAAACAAAUCA
...............(((............)))...(((((((((....((((.....))))..(((((.((((.....)))).))))).....)))))))))................. ( -33.20)
>DroEre_CAF1 56222 118 - 1
AA--AUAUCAAUACAUGGUCAGAACGAUUUCCAAUAAGCCAGCACGUUCAUUGGAUCACAAUAAUGCCCAUUCAAGCGACGGGCGAGCACAGCUGUGCCGGCUAAAACAAAAACAAAUCA
..--...........(((((.(((....)))......((((((..((((((((.....))))...((((..((....)).))))))))...)))).)).)))))................ ( -24.50)
>DroYak_CAF1 56121 118 - 1
AA--AUAUCAAUACAUGGUCAGGACGAUUUCCAAUAAGCCAGCACGUUCAUUGGAUCACAAUAAUGCCCAUUGAAGCGACGGGCGAGCACAGCUGUGCCGGCUAAAACAAAAACAAAUCA
..--...........(((((.(((.....))).....((((((..((((((((.....))))...((((.(((...))).))))))))...)))).)).)))))................ ( -28.40)
>consensus
AAAAACAUCAAUACAUGGUCAGAACGAUUUCCAAUAAGCCGGCACGUUCAUUGGAUCACAAUAAUGCCCAUUCGAGCGACGGGCGGGCACAGCUGUGCCGGCUAAAACAAAAACAAAUCA
...............(((............)))...(((((((((((((((((.....))))...((((.((.....)).))))))))......)))))))))................. (-26.38 = -26.74 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:22 2006