Locus 7061

Sequence ID	3L_DroMel_CAF1
Location	19,119,801 – 19,120,008
Length	207
Max. P	0.861074

overview

Window 5

Location	19,119,801 – 19,119,908
Length	107
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	90.58
Mean single sequence MFE	-25.72
Consensus MFE	-20.40
Energy contribution	-20.60
Covariance contribution	0.20
Combinations/Pair	1.07
Mean z-score	-1.77
Structure conservation index	0.79
SVM decision value	0.73
SVM RNA-class probability	0.836069
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19119801 107 - 23771897
AAUUGCUAGCCAUCGAGAA------UGUUGCCAAUUCGCGUUGGCGACUCGUAAAUAAAUAGAACUAAUGUCUACGAAUUAAUUCCGAAUAUUCGGUCGAAGCAAACAAAUCG
..(((((.....((((...------.(((((((((....)))))))))(((((.(((...........))).))))).......((((....)))))))))))))........ ( -25.10)
>DroSec_CAF1 7330 106 - 1
AAUUGCUUGCCAUCGAGAA------UGUUGCCAAUUCGCGUUGGCGACUCGUAAAUAAAUAG-ACUAAUGUCCGCGAAUUAAUUCCGAAUAUUCGGUCAAAGCAAACAAAUCG
..((((((((((.((.(((------(.......)))).)).))))................(-((((((((.((.(((....))))).))))).)))).))))))........ ( -26.80)
>DroSim_CAF1 8265 106 - 1
AAUUGCUAGCCAUCGAGAA------UGUUGCCAAUUCGCGUUGGCGACUCGUAAAUAAAUAG-ACUAAUGUCUGCGAAUUAAUUCCGAAUAUUCGGUCAAAGCAAACAAAUCG
..(((((.((((.((.(((------(.......)))).)).))))(((...........(((-((....)))))(((((...........))))))))..)))))........ ( -27.20)
>DroEre_CAF1 794 107 - 1
AAUGGCUACCCAUCGAGUA------UGUUGCCAAUUCGCGUUGGCGACUCGUAAAUAAAUUAAACUAAUGUCUGUGAAUUAAUUGCGAAAAUUCGGUCAAAGCAAACAAAUCG
....(((....(((((((.------.(((((((((....)))))))))((((((.(((.(((.((....))...))).))).))))))..)))))))...))).......... ( -26.70)
>DroYak_CAF1 5679 113 - 1
AAUUGCUAACCAUCGAGUACCCAAAUGAUGCCAAUUCGCGUUGGCGACUCGUAAAUAAAUAAUACUGAUGUCUGUGAAUUAGUUCCGAAAAUUCGGUCAAAGCAAACAAAUCG
..(((((....(((((((......(((((((((((....)))))))..))))...........((((((........)))))).......)))))))...)))))........ ( -22.80)
>consensus
AAUUGCUAGCCAUCGAGAA______UGUUGCCAAUUCGCGUUGGCGACUCGUAAAUAAAUAG_ACUAAUGUCUGCGAAUUAAUUCCGAAUAUUCGGUCAAAGCAAACAAAUCG
..(((((....((((((.........(((((((((....)))))))))(((((.(((...........))).)))))..............))))))...)))))........ (-20.40 = -20.60 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	19,119,908 – 19,120,008
Length	100
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	81.53
Mean single sequence MFE	-23.83
Consensus MFE	-15.14
Energy contribution	-15.70
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-2.14
Structure conservation index	0.64
SVM decision value	0.83
SVM RNA-class probability	0.861074
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19119908 100 - 23771897
AAAUAAAUAAAAAAGUCCUU----------UUUGGCAGGCCGCAACU-----CUAAAAAUGGCAAUUUAUGAGCCAUGCGAAGCGUUGUUUGCCUUGCAUUAAAUUGCAUAAAUU
..............((..((----------(...((((((.(((((.-----((....(((((.........)))))....)).)))))..))).)))...)))..))....... ( -22.80)
>DroEre_CAF1 901 98 - 1
AAAUAAAUAA--AAAUCCUU----------UUUGGCAGGCCGCAGCU-----CUAAAAAUGGCAAUUUAUGAGCCAUGAGAAGCGUUGUUUGCCUUGCAUUAAAUUGCAUAAAUU
..........--........----------...(((((((.((.(((-----((....(((((.........))))).)).))))).))))))).((((......))))...... ( -25.90)
>DroYak_CAF1 5792 98 - 1
AAAUAAAUAA--AAAUCCUU----------UUUGGCAGGCCGCAACU-----CUAAAAAUGGCAAUUUAUGAGCCAUGAGAAGCGUUGUUUGCCUUGCAUUAAAUUGCAUAAAUU
..........--........----------...((((((((((..((-----(.....(((((.........))))))))..)))..))))))).((((......))))...... ( -24.70)
>DroAna_CAF1 7471 109 - 1
AAAUAAAUAA--AAAUCCUAAAAGCGGCCAUCCAGCAGGCAGCUCCUCCUUACUAAAAAUGA----GUGUGAGCCGUGUGAGUCGUUGUUUGCAUUGCAUUAAAUUGCAUAAACU
..........--.............((....)).(((((((((..((((((((.........----..)))))......)))..)))))))))..((((......))))...... ( -21.90)
>consensus
AAAUAAAUAA__AAAUCCUU__________UUUGGCAGGCCGCAACU_____CUAAAAAUGGCAAUUUAUGAGCCAUGAGAAGCGUUGUUUGCCUUGCAUUAAAUUGCAUAAAUU
.................................(((((((.((...............(((((.........)))))(.....))).))))))).((((......))))...... (-15.14 = -15.70 +   0.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:39 2006