Locus 5446

Sequence ID	2L_DroMel_CAF1
Location	15,521,439 – 15,521,570
Length	131
Max. P	0.668025

overview

Window 5

Location	15,521,439 – 15,521,531
Length	92
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	79.26
Mean single sequence MFE	-22.26
Consensus MFE	-13.01
Energy contribution	-12.20
Covariance contribution	-0.80
Combinations/Pair	1.21
Mean z-score	-1.73
Structure conservation index	0.58
SVM decision value	0.23
SVM RNA-class probability	0.644190
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15521439 92 - 22407834
CAUUAAG--------------CGACUAAUGAAUGCAACAAGCAAUCAGGCAACAAACUGUUGCAUUCAAAGCACUACUAAUGAG-UGGUUGAAUUCAAUUUAAACGA---
......(--------------((((...(((.(((.....))).)))(....).....)))))((((((..((((.(....)))-)).)))))).............--- ( -19.90)
>DroPse_CAF1 73941 106 - 1
CAUUAAGUGCCGAGGAGAUGCCGUCUCGUGAAUGCAAC----AAUCAGGCAGCAAACUGUUGCACUCAAAGCCCUCCUAAUGAACUGGGGGACUACAAUCUAAAUUUAUU
.....(((((((((..(....)..))))(((.((((((----(..............))))))).)))..))(((((.........))))))))................ ( -23.34)
>DroSim_CAF1 26607 92 - 1
CAUUAAG--------------CGACUAAUGAAUGCAACAAGCAAUCAGGCAACAAACUGUUGCAUUCAAAGCACUACUAAUGAG-UGGUUGAAUUCAAUUUAGACGA---
.......--------------((.(((((((((.((((..((((.(((........)))))))........((((.(....)))-)))))).)))))..)))).)).--- ( -21.70)
>DroEre_CAF1 26522 92 - 1
CAUUAAG--------------CGACUAAUGAAUGCAACAAGCAAUCAGGCAACAAACUGUUGCAUUCAAAGCACUACUAAUGAG-UGGUUGAAUUCAAUUUAGACGA---
.......--------------((.(((((((((.((((..((((.(((........)))))))........((((.(....)))-)))))).)))))..)))).)).--- ( -21.70)
>DroYak_CAF1 26859 92 - 1
CAUUAAG--------------CGACUAAUGAAUGCAACAAGCAAUCAGGCAACAAACUGUUGCGUUCAAAGCACUACUAAUGAG-UGGUUGAAUUCAAUUUAGACGA---
.......--------------((.(((((((((.((((..((((.(((........)))))))........((((.(....)))-)))))).)))))..)))).)).--- ( -21.70)
>DroPer_CAF1 72599 106 - 1
CAUUAAGUGCCGGGGAGAUGCCGUCUCGUGAAUGCAAC----AAUCAGGCAGCAAACUGUUGCACUCAAAGCCCUCCUAAUGAACUGGGGGACUACAAUCUAAAUUUAUU
.....(((.((((((((((...))))).(((.((((((----(..............))))))).)))...))).((((......)))))))))................ ( -25.24)
>consensus
CAUUAAG______________CGACUAAUGAAUGCAACAAGCAAUCAGGCAACAAACUGUUGCAUUCAAAGCACUACUAAUGAG_UGGUUGAAUUCAAUUUAAACGA___
......................((....(((((((((((..................)))))))))))...((..((((......))))))...)).............. (-13.01 = -12.20 +  -0.80)

alignment

secondary structure

dotplot

Window 6

Location	15,521,472 – 15,521,570
Length	98
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	82.53
Mean single sequence MFE	-27.55
Consensus MFE	-18.75
Energy contribution	-18.53
Covariance contribution	-0.22
Combinations/Pair	1.05
Mean z-score	-1.94
Structure conservation index	0.68
SVM decision value	0.28
SVM RNA-class probability	0.668025
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15521472 98 - 22407834
UUAGUUCAAUUUGGGUUGCAUAAAAGUGCAUGGCAAUUGCAUUAAG--------------CGACUAAUGAAUGCAACAAGCAAUCAGGCAACAAACUGUUGCAUUCAAAGCA
...(((.......((((((.....((((((.......))))))..)--------------)))))..(((((((((((........(....)....))))))))))).))). ( -25.50)
>DroPse_CAF1 73978 107 - 1
UUGCCUCGGGCU-UGUUGCAUAAGAGUGCAUGGCAAUUGCAUUAAGUGCCGAGGAGAUGCCGUCUCGUGAAUGCAAC----AAUCAGGCAGCAAACUGUUGCACUCAAAGCC
........((((-((((((((...((((((.......))))))......((((..(....)..))))...)))))))----......(((((.....))))).....))))) ( -31.90)
>DroSim_CAF1 26640 98 - 1
UUAGUUCAAUUUGGGUUGCAUAAAAGUGCAUGGCAAUUGCAUUAAG--------------CGACUAAUGAAUGCAACAAGCAAUCAGGCAACAAACUGUUGCAUUCAAAGCA
...(((.......((((((.....((((((.......))))))..)--------------)))))..(((((((((((........(....)....))))))))))).))). ( -25.50)
>DroEre_CAF1 26555 98 - 1
UUAGUUCAAUUUGGGUUGCAUAAAAGUGCAUGGCAAUUGCAUUAAG--------------CGACUAAUGAAUGCAACAAGCAAUCAGGCAACAAACUGUUGCAUUCAAAGCA
...(((.......((((((.....((((((.......))))))..)--------------)))))..(((((((((((........(....)....))))))))))).))). ( -25.50)
>DroYak_CAF1 26892 98 - 1
UUAGUUCAAUUUGGGUUGCAUAAAAGUGCAUGGCAAUUGCAUUAAG--------------CGACUAAUGAAUGCAACAAGCAAUCAGGCAACAAACUGUUGCGUUCAAAGCA
...(((.......((((((.....((((((.......))))))..)--------------)))))..(((((((((((........(....)....))))))))))).))). ( -25.10)
>DroPer_CAF1 72636 107 - 1
UUGCCUCGGGCU-UGUUGCAUAAGAGUGCAUGGCAAUUGCAUUAAGUGCCGGGGAGAUGCCGUCUCGUGAAUGCAAC----AAUCAGGCAGCAAACUGUUGCACUCAAAGCC
........((((-((((((((..(((.((((..(..(.((((...)))).)..)..))))...)))....)))))))----......(((((.....))))).....))))) ( -31.80)
>consensus
UUAGUUCAAUUUGGGUUGCAUAAAAGUGCAUGGCAAUUGCAUUAAG______________CGACUAAUGAAUGCAACAAGCAAUCAGGCAACAAACUGUUGCAUUCAAAGCA
..............(((((((...((((((.......))))))....................(....).)))))))..........(((((.....))))).......... (-18.75 = -18.53 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:22 2006