Locus 5218

Sequence ID	3R_DroMel_CAF1
Location	13,662,903 – 13,662,994
Length	91
Max. P	0.994841

overview

Window 3

Location	13,662,903 – 13,662,994
Length	91
Sequences	5
Columns	93
Reading direction	forward
Mean pairwise identity	81.81
Mean single sequence MFE	-20.98
Consensus MFE	-12.73
Energy contribution	-13.36
Covariance contribution	0.63
Combinations/Pair	1.06
Mean z-score	-1.86
Structure conservation index	0.61
SVM decision value	0.15
SVM RNA-class probability	0.607969
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13662903 91 + 27905053
UUUCCUUUCCACAC-CCCCCAAGAAGCAAAGAAAAACUUGGAAAGGUUGGCACAUUUUCCACCUCUCCCGGUCGAAGUUGGGGGCGAAAA-AA
.............(-(((((((...((.......(((((....))))).))....((((.(((......))).))))))))))).)....-.. ( -22.40)
>DroSec_CAF1 27955 72 + 1
UUCCCUUUC-----GCCCCCAAGAAGCAAAGAAAAACUUGGAAAGUU----------------UCUCCCUGUUGAAGUUGGGGACGAAAAAAA
.....((((-----(.((((((..((((..((.(((((.....))))----------------).))..))))....)))))).))))).... ( -21.10)
>DroSim_CAF1 27939 91 + 1
UUCCCUUUCCAUACCCCCCCAAGAAGCAAAGAAAAACUUGGAAAGGUUGGCACAUUUUCCACCUCUCCCUGUCGAAGUUGGGGGCGAAA--AA
.............(.(((((((......(((.....)))(((.((((.((........)))))).))).........))))))).)...--.. ( -21.10)
>DroEre_CAF1 32054 88 + 1
UUCCCUUUCCACAC--CCCCAAGAAGCAUAGAAAAACUUGGAAAGGUUGGCACAUUUUCCACCUCUCCCUGUCGAAGUUGGGGG--AAAA-AA
.............(--((((((...(.((((........(((.((((.((........)))))).))))))))....)))))))--....-.. ( -22.00)
>DroYak_CAF1 28387 87 + 1
UUC-CUUUCCACAC--CCCCAAGAAGCAUAGAAAAACUUGGAAAGGUUGGUACAUUUUCUACCUCUCCCUUUCGAAGUUGGGUC--AAAA-AA
...-..........--..............((..(((((.((((((..((((.......))))....)))))).)))))...))--....-.. ( -18.30)
>consensus
UUCCCUUUCCACAC_CCCCCAAGAAGCAAAGAAAAACUUGGAAAGGUUGGCACAUUUUCCACCUCUCCCUGUCGAAGUUGGGGGCGAAAA_AA
................((((((.(((..........)))(((.(((.(((........)))))).))).........)))))).......... (-12.73 = -13.36 +   0.63)

alignment

secondary structure

dotplot

Window 4

Location	13,662,903 – 13,662,994
Length	91
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	81.81
Mean single sequence MFE	-30.50
Consensus MFE	-19.09
Energy contribution	-20.36
Covariance contribution	1.27
Combinations/Pair	1.05
Mean z-score	-3.31
Structure conservation index	0.63
SVM decision value	2.52
SVM RNA-class probability	0.994841
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13662903 91 - 27905053
UU-UUUUCGCCCCCAACUUCGACCGGGAGAGGUGGAAAAUGUGCCAACCUUUCCAAGUUUUUCUUUGCUUCUUGGGGG-GUGUGGAAAGGAAA
((-((..(((((((...........((((((((((........)).))))))))((((........))))....))))-)))..))))..... ( -32.30)
>DroSec_CAF1 27955 72 - 1
UUUUUUUCGUCCCCAACUUCAACAGGGAGA----------------AACUUUCCAAGUUUUUCUUUGCUUCUUGGGGGC-----GAAAGGGAA
((((((((((((((((......((((((((----------------((((.....))))))))))))....))))))))-----)))))))). ( -32.90)
>DroSim_CAF1 27939 91 - 1
UU--UUUCGCCCCCAACUUCGACAGGGAGAGGUGGAAAAUGUGCCAACCUUUCCAAGUUUUUCUUUGCUUCUUGGGGGGGUAUGGAAAGGGAA
((--((((((((((...........((((((((((........)).))))))))((((........)))).....))))))..)))))).... ( -29.80)
>DroEre_CAF1 32054 88 - 1
UU-UUUU--CCCCCAACUUCGACAGGGAGAGGUGGAAAAUGUGCCAACCUUUCCAAGUUUUUCUAUGCUUCUUGGGG--GUGUGGAAAGGGAA
..-..((--(((........(((..((((((((((........)).))))))))..)))(((((((((((.....))--)))))))))))))) ( -31.70)
>DroYak_CAF1 28387 87 - 1
UU-UUUU--GACCCAACUUCGAAAGGGAGAGGUAGAAAAUGUACCAACCUUUCCAAGUUUUUCUAUGCUUCUUGGGG--GUGUGGAAAG-GAA
..-....--...(((((((.((((((....((((.......))))..)))))).)))))(((((((((((.....))--))))))))))-).. ( -25.80)
>consensus
UU_UUUUCGCCCCCAACUUCGACAGGGAGAGGUGGAAAAUGUGCCAACCUUUCCAAGUUUUUCUUUGCUUCUUGGGGG_GUGUGGAAAGGGAA
.........(((((((.........((((((((((........))).)))))))((((........)))).)))))))............... (-19.09 = -20.36 +   1.27)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:21 2006