Locus 2804

Sequence ID	2L_DroMel_CAF1
Location	7,958,144 – 7,958,259
Length	115
Max. P	0.993642

overview

Window 4

Location	7,958,144 – 7,958,238
Length	94
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	85.73
Mean single sequence MFE	-23.18
Consensus MFE	-17.98
Energy contribution	-18.02
Covariance contribution	0.04
Combinations/Pair	1.05
Mean z-score	-2.57
Structure conservation index	0.78
SVM decision value	1.85
SVM RNA-class probability	0.979986
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7958144 94 + 22407834
GUUA-------------UUCGAUCCCGAACUCAUUUCUUGCCCUGCA---CCAACUGGCAACAUCAAUCUGGUCAAGAUGUUGCCACAUUGAAUUAAAAUAUUCAAAUGC
....-------------((((....))))...............(((---.....((((((((((...........))))))))))..((((((......)))))).))) ( -21.10)
>DroSec_CAF1 129466 91 + 1
GUUG-------------UUCGAUCCCGAACUCAUUUCUUGCCAUGC------AACUGGCAACAUCAAUCUGGUCAAGAUGUUGCCACAUUGAAUUAAAAUAUUCAAAUGC
...(-------------((((....)))))..............((------(..((((((((((...........))))))))))..((((((......)))))).))) ( -24.50)
>DroSim_CAF1 129535 97 + 1
GUUG-------------UUCGAUCCCGAACUAAUUUCUUGCCAUGCACCACCAACUGGCAACAUCAAUCUGGUCAAGAUGUUGCCACAUUGAAUUAAAAUAUUCAAAUGC
...(-------------((((....)))))..............(((........((((((((((...........))))))))))..((((((......)))))).))) ( -24.20)
>DroEre_CAF1 131324 107 + 1
GUUUUAAACAGAUCUCUGUCGAUGCCGAACUCAUUUCUUGCCAUGCA---CCAACUGGCAACAUCAAUCUGGGCAAGAUGUUGCCACAUUAAAUUAAAAUAUUCAAAUGC
(((((((((((....)))).((((..............(((...)))---.....((((((((((...........))))))))))))))...))))))).......... ( -21.20)
>DroYak_CAF1 134693 105 + 1
GUUUUAAACAGAUCU--UUCGAUCGUGAACUCAUUUCUCGCCAUGCA---CCAACUGGCAACAUCAAUGUGGGCAAGAUGUUGCCACAUUGAAUUAAAAUAUUCAAAUGC
..........((((.--...))))((((.........))))...(((---.....((((((((((..((....)).))))))))))..((((((......)))))).))) ( -24.90)
>consensus
GUUG_____________UUCGAUCCCGAACUCAUUUCUUGCCAUGCA___CCAACUGGCAACAUCAAUCUGGUCAAGAUGUUGCCACAUUGAAUUAAAAUAUUCAAAUGC
..................(((....)))................((.........((((((((((...........))))))))))..((((((......))))))..)) (-17.98 = -18.02 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	7,958,144 – 7,958,238
Length	94
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	85.73
Mean single sequence MFE	-28.86
Consensus MFE	-20.22
Energy contribution	-20.06
Covariance contribution	-0.16
Combinations/Pair	1.06
Mean z-score	-2.55
Structure conservation index	0.70
SVM decision value	1.16
SVM RNA-class probability	0.924607
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7958144 94 - 22407834
GCAUUUGAAUAUUUUAAUUCAAUGUGGCAACAUCUUGACCAGAUUGAUGUUGCCAGUUGG---UGCAGGGCAAGAAAUGAGUUCGGGAUCGAA-------------UAAC
(((((.((((......)))))))))(((((((((...........)))))))))..((((---(.(.((((.(....)..)))).).))))).-------------.... ( -26.10)
>DroSec_CAF1 129466 91 - 1
GCAUUUGAAUAUUUUAAUUCAAUGUGGCAACAUCUUGACCAGAUUGAUGUUGCCAGUU------GCAUGGCAAGAAAUGAGUUCGGGAUCGAA-------------CAAC
(((.((((((......))))))..((((((((((...........))))))))))..)------))..............(((((....))))-------------)... ( -26.60)
>DroSim_CAF1 129535 97 - 1
GCAUUUGAAUAUUUUAAUUCAAUGUGGCAACAUCUUGACCAGAUUGAUGUUGCCAGUUGGUGGUGCAUGGCAAGAAAUUAGUUCGGGAUCGAA-------------CAAC
((((((((((......))))))..((((((((((...........)))))))))).......))))..............(((((....))))-------------)... ( -27.70)
>DroEre_CAF1 131324 107 - 1
GCAUUUGAAUAUUUUAAUUUAAUGUGGCAACAUCUUGCCCAGAUUGAUGUUGCCAGUUGG---UGCAUGGCAAGAAAUGAGUUCGGCAUCGACAGAGAUCUGUUUAAAAC
...((((((((..((.........((((((((((...........))))))))))(((((---(((..(((.(....)..)))..))))))))...))..)))))))).. ( -31.50)
>DroYak_CAF1 134693 105 - 1
GCAUUUGAAUAUUUUAAUUCAAUGUGGCAACAUCUUGCCCACAUUGAUGUUGCCAGUUGG---UGCAUGGCGAGAAAUGAGUUCACGAUCGAA--AGAUCUGUUUAAAAC
...((((((((.......((((((((((((....))).)))))))))(.((((((((...---.)).)))))).)...........((((...--.)))))))))))).. ( -32.40)
>consensus
GCAUUUGAAUAUUUUAAUUCAAUGUGGCAACAUCUUGACCAGAUUGAUGUUGCCAGUUGG___UGCAUGGCAAGAAAUGAGUUCGGGAUCGAA_____________AAAC
((..((((((......))))))..((((((((((...........)))))))))).........))............................................ (-20.22 = -20.06 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	7,958,169 – 7,958,259
Length	90
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	86.65
Mean single sequence MFE	-29.14
Consensus MFE	-20.82
Energy contribution	-21.86
Covariance contribution	1.04
Combinations/Pair	1.04
Mean z-score	-3.08
Structure conservation index	0.71
SVM decision value	1.80
SVM RNA-class probability	0.977791
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7958169 90 + 22407834
UGCCCUGCA---CCAACUGGCAACAUCAAUCUGGUCAAGAUGUUGCCACAUUGAAUUAAAAUAUUCAAAUGCAACCA--------AGUGGAUG-GGAGUGGG
...((..(.---((...((((((((((...........))))))))))..((((((......))))))...((.((.--------...)).))-)).)..)) ( -27.60)
>DroSec_CAF1 129491 96 + 1
UGCCAUGC------AACUGGCAACAUCAAUCUGGUCAAGAUGUUGCCACAUUGAAUUAAAAUAUUCAAAUGCAACCAUCCAGCCAAGUGGAUGGGGAGUGGG
..((((((------(..((((((((((...........))))))))))..((((((......)))))).)))..(((((((......)))))))...)))). ( -36.30)
>DroSim_CAF1 129560 92 + 1
UGCCAUGCACCACCAACUGGCAACAUCAAUCUGGUCAAGAUGUUGCCACAUUGAAUUAAAAUAUUCAAAUGCAACCAUCC----------AUGGGGAGUGGG
..((((...((.(((..((((((((((...........))))))))))..((((((......))))))............----------.))))).)))). ( -28.20)
>DroEre_CAF1 131362 94 + 1
UGCCAUGCA---CCAACUGGCAACAUCAAUCUGGGCAAGAUGUUGCCACAUUAAAUUAAAAUAUUCAAAUGCAAGCAGCC----AAGAAGCUG-GGAGUGGG
..((((...---((...((((((((((...........))))))))))...........................((((.----.....))))-)).)))). ( -25.70)
>DroYak_CAF1 134729 94 + 1
CGCCAUGCA---CCAACUGGCAACAUCAAUGUGGGCAAGAUGUUGCCACAUUGAAUUAAAAUAUUCAAAUGCAGCCAGCC----AAGAAGAUG-GGAGUGGG
..((((...---(((.(((((((((((..((....)).)))))))))...((((((......))))))............----....)).))-)..)))). ( -27.90)
>consensus
UGCCAUGCA___CCAACUGGCAACAUCAAUCUGGUCAAGAUGUUGCCACAUUGAAUUAAAAUAUUCAAAUGCAACCAGCC____AAGAAGAUG_GGAGUGGG
..((((((.........((((((((((...........))))))))))..((((((......))))))..))...((((..........))))....)))). (-20.82 = -21.86 +   1.04)

alignment

secondary structure

dotplot

Window 7

Location	7,958,169 – 7,958,259
Length	90
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	86.65
Mean single sequence MFE	-30.32
Consensus MFE	-22.70
Energy contribution	-23.50
Covariance contribution	0.80
Combinations/Pair	1.12
Mean z-score	-3.29
Structure conservation index	0.75
SVM decision value	2.41
SVM RNA-class probability	0.993642
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7958169 90 - 22407834
CCCACUCC-CAUCCACU--------UGGUUGCAUUUGAAUAUUUUAAUUCAAUGUGGCAACAUCUUGACCAGAUUGAUGUUGCCAGUUGG---UGCAGGGCA
(((....(-((......--------))).(((((((((((......))))))..((((((((((...........))))))))))....)---))))))).. ( -29.50)
>DroSec_CAF1 129491 96 - 1
CCCACUCCCCAUCCACUUGGCUGGAUGGUUGCAUUUGAAUAUUUUAAUUCAAUGUGGCAACAUCUUGACCAGAUUGAUGUUGCCAGUU------GCAUGGCA
.(((....(((((((......))))))).((((.((((((......))))))..((((((((((...........))))))))))..)------)))))).. ( -33.70)
>DroSim_CAF1 129560 92 - 1
CCCACUCCCCAU----------GGAUGGUUGCAUUUGAAUAUUUUAAUUCAAUGUGGCAACAUCUUGACCAGAUUGAUGUUGCCAGUUGGUGGUGCAUGGCA
.(((..(.((((----------.(((....(((((.((((......)))))))))(((((((((...........))))))))).))).)))).)..))).. ( -29.10)
>DroEre_CAF1 131362 94 - 1
CCCACUCC-CAGCUUCUU----GGCUGCUUGCAUUUGAAUAUUUUAAUUUAAUGUGGCAACAUCUUGCCCAGAUUGAUGUUGCCAGUUGG---UGCAUGGCA
.(((....-(((((....----)))))..(((((((((((......))))))..((((((((((...........))))))))))....)---))))))).. ( -28.20)
>DroYak_CAF1 134729 94 - 1
CCCACUCC-CAUCUUCUU----GGCUGGCUGCAUUUGAAUAUUUUAAUUCAAUGUGGCAACAUCUUGCCCACAUUGAUGUUGCCAGUUGG---UGCAUGGCG
.......(-((((...(.----.((((((.(((((.((((......))))((((((((((....))).)))))))))))).))))))..)---.).)))).. ( -31.10)
>consensus
CCCACUCC_CAUCCACUU____GGAUGGUUGCAUUUGAAUAUUUUAAUUCAAUGUGGCAACAUCUUGACCAGAUUGAUGUUGCCAGUUGG___UGCAUGGCA
.((......(((((........)))))..(((..((((((......))))))..((((((((((...........)))))))))).........))).)).. (-22.70 = -23.50 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:38 2006