Locus 5824

Sequence ID	2L_DroMel_CAF1
Location	16,498,882 – 16,499,000
Length	118
Max. P	0.752110

overview

Window 4

Location	16,498,882 – 16,498,972
Length	90
Sequences	6
Columns	90
Reading direction	reverse
Mean pairwise identity	81.99
Mean single sequence MFE	-28.85
Consensus MFE	-19.65
Energy contribution	-21.15
Covariance contribution	1.50
Combinations/Pair	1.22
Mean z-score	-1.38
Structure conservation index	0.68
SVM decision value	-0.05
SVM RNA-class probability	0.506717
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16498882 90 - 22407834
UGCUAGCAUUGUGACCCGCACUGUGCGUACGUGUUGGUCCGCAUGUGCAAAUGCCUGCAGGUCACAGCAGAGUUCAAUGCGCGAUAAGCG
.(((.((..(((((((.((((.(((((.((......)).)))))))))...((....)))))))))(((........)))))....))). ( -32.60)
>DroSec_CAF1 17741 90 - 1
UGCUAGCAUUGUGACCCGCACUGUGCGUACGUGUUAGUCCGCAUAUGCAAAUGCCUGCAGGUCACAGCAGAGUUCAAUGCGCGAUAAGCG
.(((.((..(((((((.(((.((((((.((......)).)))))).((....)).))).)))))))(((........)))))....))). ( -32.20)
>DroSim_CAF1 11268 90 - 1
UGCUAGCAUUGUGACCCGCACUGUGCGUACGUGUUAGUCCGCAUAUGCAAAUGCCUGCAGGUCACAGCAGAGUUCAAUGCGCGAUAAGCG
.(((.((..(((((((.(((.((((((.((......)).)))))).((....)).))).)))))))(((........)))))....))). ( -32.20)
>DroEre_CAF1 23501 90 - 1
CGCUAGCAAUGUGACCACCACUGUGCGUACGUGUUGGUCCGCAUGUGCAAAUGCCUGCAGGUCACAGUAGAGUUCAAUGCGCGAUAAGCG
((((.((..(((((((......(((((.((......)).))))).((((......)))))))))))(((........)))))....)))) ( -29.10)
>DroWil_CAF1 66316 68 - 1
CGUGUGUC-U----AUG----UGUGUGUGGGUUUUGGU------GUG-------CUUCAGGUCAUAGUAAAGUUCAAUGCGCGAUAAGCA
.((.((((-.----..(----(((((.((..(((((.(------(((-------(.....).)))).)))))..)))))))))))).)). ( -18.30)
>DroYak_CAF1 11703 89 - 1
UGCUAGCAUUGUGAGCCCCACUGUGCGUACGUGUUGGU-CGCAUGUGCAAAUGCCUGCAGGUCACAGCAGAGUUCAAUGCGCGAUAAGCG
.....((((..(((((.(..(((((.((((((((....-.))))))))....(((....))))))))..).)))))))))((.....)). ( -28.70)
>consensus
UGCUAGCAUUGUGACCCGCACUGUGCGUACGUGUUGGUCCGCAUGUGCAAAUGCCUGCAGGUCACAGCAGAGUUCAAUGCGCGAUAAGCG
.(((.((..(((((((.....((((((.((......)).))))))((((......)))))))))))(((........)))))....))). (-19.65 = -21.15 +   1.50)

alignment

secondary structure

dotplot

Window 5

Location	16,498,903 – 16,499,000
Length	97
Sequences	5
Columns	97
Reading direction	reverse
Mean pairwise identity	85.68
Mean single sequence MFE	-29.12
Consensus MFE	-22.02
Energy contribution	-21.82
Covariance contribution	-0.20
Combinations/Pair	1.10
Mean z-score	-1.82
Structure conservation index	0.76
SVM decision value	0.48
SVM RNA-class probability	0.752110
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16498903 97 - 22407834
CACAACAAUUCAUUAAUAGCCCCUUUGUUGCUAGCAUUGUGACCCGCACUGUGCGUACGUGUUGGUCCGCAUGUGCAAAUGCCUGCAGGUCACAGCA
..((((((................))))))...((..(((((((.((((.(((((.((......)).)))))))))...((....))))))))))). ( -29.29)
>DroSec_CAF1 17762 96 - 1
CACAACAAUUCAUUAACAGCCCCU-UGUUGCUAGCAUUGUGACCCGCACUGUGCGUACGUGUUAGUCCGCAUAUGCAAAUGCCUGCAGGUCACAGCA
..((((((...............)-)))))...((..(((((((.(((.((((((.((......)).)))))).((....)).))).))))))))). ( -28.16)
>DroSim_CAF1 11289 96 - 1
CACAACAAUUCAUUAACAGCCCCU-UGUUGCUAGCAUUGUGACCCGCACUGUGCGUACGUGUUAGUCCGCAUAUGCAAAUGCCUGCAGGUCACAGCA
..((((((...............)-)))))...((..(((((((.(((.((((((.((......)).)))))).((....)).))).))))))))). ( -28.16)
>DroEre_CAF1 23522 96 - 1
CACAAUAAACAAAUAGUGUGUCCU-UGGCGCUAGCAAUGUGACCACCACUGUGCGUACGUGUUGGUCCGCAUGUGCAAAUGCCUGCAGGUCACAGUA
.............((.((((.(((-.((((...((((((((((((.(((.((....))))).)))).))))).)))...))))...))).)))).)) ( -31.20)
>DroYak_CAF1 11724 92 - 1
UACAAUAGCU---UAAUGUGAUGU-UGGUGCUAGCAUUGUGAGCCCCACUGUGCGUACGUGUUGGU-CGCAUGUGCAAAUGCCUGCAGGUCACAGCA
.......(((---....(((((((-.(((....((((.(((.....))).))))((((((((....-.))))))))....))).)))..))))))). ( -28.80)
>consensus
CACAACAAUUCAUUAAUAGCCCCU_UGUUGCUAGCAUUGUGACCCGCACUGUGCGUACGUGUUGGUCCGCAUGUGCAAAUGCCUGCAGGUCACAGCA
.................................((..(((((((.....((((((.((......)).))))))((((......))))))))))))). (-22.02 = -21.82 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:56 2006