Locus 5124

Sequence ID	2L_DroMel_CAF1
Location	14,554,887 – 14,555,002
Length	115
Max. P	0.999871

overview

Window 8

Location	14,554,887 – 14,554,981
Length	94
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	90.88
Mean single sequence MFE	-22.22
Consensus MFE	-17.71
Energy contribution	-17.52
Covariance contribution	-0.19
Combinations/Pair	1.12
Mean z-score	-2.48
Structure conservation index	0.80
SVM decision value	0.31
SVM RNA-class probability	0.684960
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14554887 94 + 22407834
AAGCCAUCAGUUGCCAGCCAGACAAUCUGUCAAACAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAA-CAGCAACAGCUGCGGAAAA
...((..((((((.......(((.....)))..........((((...((((((............))))))...-))))..)))))).)).... ( -22.60)
>DroSec_CAF1 86662 94 + 1
AAGCCAUCAGUUGCCAGCCAGACAAUCUGUCAAACAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAA-CAGCAACAGCUGCGGAAAA
...((..((((((.......(((.....)))..........((((...((((((............))))))...-))))..)))))).)).... ( -22.60)
>DroSim_CAF1 74128 94 + 1
AAGCCAUCAGUUGCCAGCCAGACAAUCUGUCAAACAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAA-CAGCAACAGCUGCGGAAAA
...((..((((((.......(((.....)))..........((((...((((((............))))))...-))))..)))))).)).... ( -22.60)
>DroEre_CAF1 81036 80 + 1
--------------CAGCCAGACAAUCUGUCAAAUAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAA-UAGCAACAGCUGCGGAAAA
--------------((((..(((.....)))..........((((...((((((............))))))...-))))....))))....... ( -17.10)
>DroYak_CAF1 77951 94 + 1
AAGCCAUCAGUUUGCAGCCAGACAAUCUGUCAAACAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAA-UAGCAACAGCUGCGGAAAA
..........((((((((..(((.....)))..........((((...((((((............))))))...-))))....))))))))... ( -23.80)
>DroAna_CAF1 25307 95 + 1
GGGCCAUCCGUCUCGGGCCAGACAAUCUGUCAAACAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAGCCAGCAACAGCUGCGGAAAA
......(((((....((((((.....(((.....))).....)))...((((((............))))))..)))(((....))))))))... ( -24.60)
>consensus
AAGCCAUCAGUUGCCAGCCAGACAAUCUGUCAAACAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAA_CAGCAACAGCUGCGGAAAA
..............((((..(((.....)))..........((((...((((((............))))))....))))....))))....... (-17.71 = -17.52 +  -0.19)

alignment

secondary structure

dotplot

Window 9

Location	14,554,912 – 14,555,002
Length	90
Sequences	6
Columns	91
Reading direction	forward
Mean pairwise identity	97.34
Mean single sequence MFE	-15.50
Consensus MFE	-15.11
Energy contribution	-14.75
Covariance contribution	-0.36
Combinations/Pair	1.12
Mean z-score	-2.30
Structure conservation index	0.97
SVM decision value	4.32
SVM RNA-class probability	0.999871
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14554912 90 + 22407834
UCUGUCAAACAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAA-CAGCAACAGCUGCGGAAAAACUCCUCAUUUCACUCUCCAC
.........((((...((((...((((((............))))))...-))))....)))).(((.....)))................ ( -16.10)
>DroSec_CAF1 86687 90 + 1
UCUGUCAAACAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAA-CAGCAACAGCUGCGGAAAAACUCCUCAUUUCACUCUCCAC
.........((((...((((...((((((............))))))...-))))....)))).(((.....)))................ ( -16.10)
>DroSim_CAF1 74153 90 + 1
UCUGUCAAACAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAA-CAGCAACAGCUGCGGAAAAACUCCUCAUUUCACUCUCCAC
.........((((...((((...((((((............))))))...-))))....)))).(((.....)))................ ( -16.10)
>DroEre_CAF1 81047 89 + 1
UCUGUCAAAUAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAA-UAGCAACAGCUGCGGAAAAACUCCUCAU-UCACUCUUCAC
(((((......(((.....))).((((((............))))))...-.(((....))))))))............-........... ( -14.10)
>DroYak_CAF1 77976 90 + 1
UCUGUCAAACAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAA-UAGCAACAGCUGCGGAAAAACUCCUCAUUUCACUCUUCAC
.........((((...((((...((((((............))))))...-))))....)))).(((.....)))................ ( -14.30)
>DroAna_CAF1 25332 91 + 1
UCUGUCAAACAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAGCCAGCAACAGCUGCGGAAAAACUCCUCAUUUCACUCUCCAC
..(((((...........)))))((((((............))))))..((.(((....)))))(((.....)))................ ( -16.30)
>consensus
UCUGUCAAACAGUCACGCUGACAGGCAUUUCCACUUAAAACAAUGCCAAA_CAGCAACAGCUGCGGAAAAACUCCUCAUUUCACUCUCCAC
.........((((...((((...((((((............))))))....))))....)))).(((.....)))................ (-15.11 = -14.75 +  -0.36)

alignment

secondary structure

dotplot

Window 0

Location	14,554,912 – 14,555,002
Length	90
Sequences	6
Columns	91
Reading direction	reverse
Mean pairwise identity	97.34
Mean single sequence MFE	-24.31
Consensus MFE	-22.95
Energy contribution	-22.73
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.17
Structure conservation index	0.94
SVM decision value	1.01
SVM RNA-class probability	0.900262
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14554912 90 - 22407834
GUGGAGAGUGAAAUGAGGAGUUUUUCCGCAGCUGUUGCUG-UUUGGCAUUGUUUUAAGUGGAAAUGCCUGUCAGCGUGACUGUUUGACAGA
((((((((.............)))))))).......((((-...((((((............))))))...))))....(((.....))). ( -24.42)
>DroSec_CAF1 86687 90 - 1
GUGGAGAGUGAAAUGAGGAGUUUUUCCGCAGCUGUUGCUG-UUUGGCAUUGUUUUAAGUGGAAAUGCCUGUCAGCGUGACUGUUUGACAGA
((((((((.............)))))))).......((((-...((((((............))))))...))))....(((.....))). ( -24.42)
>DroSim_CAF1 74153 90 - 1
GUGGAGAGUGAAAUGAGGAGUUUUUCCGCAGCUGUUGCUG-UUUGGCAUUGUUUUAAGUGGAAAUGCCUGUCAGCGUGACUGUUUGACAGA
((((((((.............)))))))).......((((-...((((((............))))))...))))....(((.....))). ( -24.42)
>DroEre_CAF1 81047 89 - 1
GUGAAGAGUGA-AUGAGGAGUUUUUCCGCAGCUGUUGCUA-UUUGGCAUUGUUUUAAGUGGAAAUGCCUGUCAGCGUGACUAUUUGACAGA
((.((((((.(-.(((.(.((.((((((((((...((((.-...))))..)))....))))))).)).).)))...).))).))).))... ( -22.00)
>DroYak_CAF1 77976 90 - 1
GUGAAGAGUGAAAUGAGGAGUUUUUCCGCAGCUGUUGCUA-UUUGGCAUUGUUUUAAGUGGAAAUGCCUGUCAGCGUGACUGUUUGACAGA
(((((.(((.(..(((.(.((.((((((((((...((((.-...))))..)))....))))))).)).).)))...).))).))).))... ( -22.80)
>DroAna_CAF1 25332 91 - 1
GUGGAGAGUGAAAUGAGGAGUUUUUCCGCAGCUGUUGCUGGCUUGGCAUUGUUUUAAGUGGAAAUGCCUGUCAGCGUGACUGUUUGACAGA
((((((((.............)))))))).......((((((..((((((............)))))).))))))....(((.....))). ( -27.82)
>consensus
GUGGAGAGUGAAAUGAGGAGUUUUUCCGCAGCUGUUGCUG_UUUGGCAUUGUUUUAAGUGGAAAUGCCUGUCAGCGUGACUGUUUGACAGA
((.((((((.(..(((.(.((.((((((((((...((((.....))))..)))....))))))).)).).)))...).))).))).))... (-22.95 = -22.73 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:37 2006