Locus 8254

Sequence ID	X_DroMel_CAF1
Location	20,493,969 – 20,494,069
Length	100
Max. P	0.960828

overview

Window 6

Location	20,493,969 – 20,494,069
Length	100
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	93.84
Mean single sequence MFE	-28.30
Consensus MFE	-25.56
Energy contribution	-25.67
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-1.32
Structure conservation index	0.90
SVM decision value	0.57
SVM RNA-class probability	0.786205
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20493969 100 + 22224390
GCGGCUCCUUGUGAAUGCAAAAUGGAAUGACAGCCGGCAAGGACGUUGCUGACAAACCCGAAACGCGAAAAUGUCAGCAAACAGGGCCAAGAAA---GGUUGC
((((((((((((...(((....((......))....)))......(((((((((....((.....))....)))))))))))))))........---)))))) ( -28.20)
>DroPse_CAF1 81771 103 + 1
UGGGCUCCUUGUGAAUGCAAAAUGGAAUGACAGCCGGCAAGGACGUUGCUGACAAAGCCCAAACGCGAAAAUGUCAGCGAACAUGGCCAAGAAAAAGGCUUGU
..(((((((((((..((((........)).))..).))))))).)))(((((((..((......)).....)))))))..(((.((((........))))))) ( -27.90)
>DroSec_CAF1 62315 100 + 1
GCGGCUCCUUGUGAAUGCAAAAUGGAAUGACAGCCGGCAAGGACGUUGCUGACAAACCCGAAACGCGAAAAUGUCAGCAAACAGGGCCAAGAAA---GGUUGC
((((((((((((...(((....((......))....)))......(((((((((....((.....))....)))))))))))))))........---)))))) ( -28.20)
>DroEre_CAF1 60420 100 + 1
GCGGCUCCUUGUGAAUGCAAAACGGAAUGACAGCCGGCAAGGACGUUGCUGACAAACCCGAAACGCGAAAAUGUCAGCAAACAGGGCCAAGAAA---GGUUGC
..(((((((((((....)....(((........))))))))))(.(((((((((....((.....))....)))))))))...).)))......---...... ( -28.30)
>DroYak_CAF1 62825 100 + 1
GCGGCUCCUUGUGAAUGCAAAAUGGAAUGACAGCCGGCAAGGACGUUGCUGACAAACCCGAAACGCGAAAAUGUCAGCAAACAGGGCCAAGAAA---GGUUGC
((((((((((((...(((....((......))....)))......(((((((((....((.....))....)))))))))))))))........---)))))) ( -28.20)
>DroPer_CAF1 83047 103 + 1
UGGGCUCCUUGUGAAUGCAAAAUGGAAUGACAGCCGGCAAGGACGUUGCUGACAAAGCCCAAACGCGAAAAUGUCAGCGAACAUGGCCAAGAAAAUGGCUUGU
..(((((((((((..((((........)).))..).))))))).)))(((((((..((......)).....)))))))..(((.(((((......)))))))) ( -29.00)
>consensus
GCGGCUCCUUGUGAAUGCAAAAUGGAAUGACAGCCGGCAAGGACGUUGCUGACAAACCCGAAACGCGAAAAUGUCAGCAAACAGGGCCAAGAAA___GGUUGC
..(((((((((((..((((........)).))..).)))))))..(((((((((....((.....))....))))))))).....)))............... (-25.56 = -25.67 +   0.11)

alignment

secondary structure

dotplot

Window 7

Location	20,493,969 – 20,494,069
Length	100
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	93.84
Mean single sequence MFE	-28.87
Consensus MFE	-26.67
Energy contribution	-27.33
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-1.54
Structure conservation index	0.92
SVM decision value	1.52
SVM RNA-class probability	0.960828
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20493969 100 - 22224390
GCAACC---UUUCUUGGCCCUGUUUGCUGACAUUUUCGCGUUUCGGGUUUGUCAGCAACGUCCUUGCCGGCUGUCAUUCCAUUUUGCAUUCACAAGGAGCCGC
......---......(((.....(((((((((..((((.....))))..)))))))))..((((((..(..((.((........))))..).))))))))).. ( -29.80)
>DroPse_CAF1 81771 103 - 1
ACAAGCCUUUUUCUUGGCCAUGUUCGCUGACAUUUUCGCGUUUGGGCUUUGUCAGCAACGUCCUUGCCGGCUGUCAUUCCAUUUUGCAUUCACAAGGAGCCCA
....(((........)))..((((.(((((((.....((......))..)))))))))))((((((..(..((.((........))))..).))))))..... ( -26.30)
>DroSec_CAF1 62315 100 - 1
GCAACC---UUUCUUGGCCCUGUUUGCUGACAUUUUCGCGUUUCGGGUUUGUCAGCAACGUCCUUGCCGGCUGUCAUUCCAUUUUGCAUUCACAAGGAGCCGC
......---......(((.....(((((((((..((((.....))))..)))))))))..((((((..(..((.((........))))..).))))))))).. ( -29.80)
>DroEre_CAF1 60420 100 - 1
GCAACC---UUUCUUGGCCCUGUUUGCUGACAUUUUCGCGUUUCGGGUUUGUCAGCAACGUCCUUGCCGGCUGUCAUUCCGUUUUGCAUUCACAAGGAGCCGC
......---......(((.....(((((((((..((((.....))))..)))))))))..((((((..(..((.((........))))..).))))))))).. ( -29.80)
>DroYak_CAF1 62825 100 - 1
GCAACC---UUUCUUGGCCCUGUUUGCUGACAUUUUCGCGUUUCGGGUUUGUCAGCAACGUCCUUGCCGGCUGUCAUUCCAUUUUGCAUUCACAAGGAGCCGC
......---......(((.....(((((((((..((((.....))))..)))))))))..((((((..(..((.((........))))..).))))))))).. ( -29.80)
>DroPer_CAF1 83047 103 - 1
ACAAGCCAUUUUCUUGGCCAUGUUCGCUGACAUUUUCGCGUUUGGGCUUUGUCAGCAACGUCCUUGCCGGCUGUCAUUCCAUUUUGCAUUCACAAGGAGCCCA
....((((......))))..((((.(((((((.....((......))..)))))))))))((((((..(..((.((........))))..).))))))..... ( -27.70)
>consensus
GCAACC___UUUCUUGGCCCUGUUUGCUGACAUUUUCGCGUUUCGGGUUUGUCAGCAACGUCCUUGCCGGCUGUCAUUCCAUUUUGCAUUCACAAGGAGCCGC
...............(((...(((.(((((((..((((.....))))..)))))))))).((((((..(..((.((........))))..).))))))))).. (-26.67 = -27.33 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:59:27 2006