Locus 4807

Sequence ID	3L_DroMel_CAF1
Location	13,434,092 – 13,434,204
Length	112
Max. P	0.915681

overview

Window 7

Location	13,434,092 – 13,434,204
Length	112
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	92.66
Mean single sequence MFE	-25.80
Consensus MFE	-23.16
Energy contribution	-23.98
Covariance contribution	0.81
Combinations/Pair	1.03
Mean z-score	-1.90
Structure conservation index	0.90
SVM decision value	1.10
SVM RNA-class probability	0.915681
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13434092 112 + 23771897
CAAGGACACUGUCACACAAAGGAGAACCCUCAUCAGUUGCAUGAAAUAAUUCCGUUUAAAUUAAGCGCCCCCCUGACAAA-AAGGAGCAGCAUUUCACGCGAUUCCCGUCCC--C
...((((..............(((....)))...((((((.((((((......(((((...)))))((..((((......-.))).)..)))))))).))))))...)))).--. ( -24.50)
>DroSim_CAF1 33161 112 + 1
CAAGGACACUUUCACACAAAGGAGAACCCUCAUCAGUUGCAUGAAAUAAUUCCGUUUAAAUUAAGCGCCCUCCUGACAAA-AAGGAGCAGCAUUUCACGCGAUUCUCGUCCC--C
...((((.((((.....))))((((..........(((((.((((((......(((((...)))))((.(((((......-.)))))..)))))))).))))))))))))).--. ( -28.60)
>DroEre_CAF1 32368 114 + 1
CAAGGACACUGACACACAAAGGAGUCCCCUCAUCCGUUGCAUGAAAUAAUUUCGUUUAAAUUAAGCUCCCUCCUGACAAA-AAGGAGCAGCAUUUUACGCGAUUCCCGUCCCCGC
...((((.............(((.........)))(((((.(((((((((((.....)))))).(((..(((((......-.))))).))).))))).)))))....)))).... ( -24.40)
>DroYak_CAF1 31620 113 + 1
CAAGGACACUGUCACACAAAGGAGACCCCUCGUCAGUUGCAUGAAAUAAUUUCGUUUAAAUUAAGCGCCCUCCUCACAAAAAAGGAGCAGCAUUUCACGCCAUUCCCGUCCC--C
...((((((((.(.(.....)(((....)))).)))).((.((((((......(((((...)))))((.(((((........)))))..)))))))).)).......)))).--. ( -25.70)
>consensus
CAAGGACACUGUCACACAAAGGAGAACCCUCAUCAGUUGCAUGAAAUAAUUCCGUUUAAAUUAAGCGCCCUCCUGACAAA_AAGGAGCAGCAUUUCACGCGAUUCCCGUCCC__C
...((((..............(((....)))...((((((.((((((......(((((...)))))((.(((((........)))))..)))))))).))))))...)))).... (-23.16 = -23.98 +   0.81)

alignment

secondary structure

dotplot

Window 8

Location	13,434,092 – 13,434,204
Length	112
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	92.66
Mean single sequence MFE	-37.15
Consensus MFE	-30.62
Energy contribution	-30.25
Covariance contribution	-0.38
Combinations/Pair	1.09
Mean z-score	-1.88
Structure conservation index	0.82
SVM decision value	0.56
SVM RNA-class probability	0.783127
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13434092 112 - 23771897
G--GGGACGGGAAUCGCGUGAAAUGCUGCUCCUU-UUUGUCAGGGGGGCGCUUAAUUUAAACGGAAUUAUUUCAUGCAACUGAUGAGGGUUCUCCUUUGUGUGACAGUGUCCUUG
(--(((((.......((((((((.((.(((((((-(.....)))))))))).((((((.....)))))))))))))).(((((..((((....))))..)....)))))))))). ( -37.30)
>DroSim_CAF1 33161 112 - 1
G--GGGACGAGAAUCGCGUGAAAUGCUGCUCCUU-UUUGUCAGGAGGGCGCUUAAUUUAAACGGAAUUAUUUCAUGCAACUGAUGAGGGUUCUCCUUUGUGUGAAAGUGUCCUUG
(--((((((((((((((((((((.(((.(((((.-......))))))))...((((((.....))))))))))))))..((....)))))))))((((.....)))).)))))). ( -35.70)
>DroEre_CAF1 32368 114 - 1
GCGGGGACGGGAAUCGCGUAAAAUGCUGCUCCUU-UUUGUCAGGAGGGAGCUUAAUUUAAACGAAAUUAUUUCAUGCAACGGAUGAGGGGACUCCUUUGUGUGUCAGUGUCCUUG
.((((((((.((...((((.((((...(((((((-((.....)))))))))...))))....(((.....))))))).(((((.(((....))).)))))...))..)))))))) ( -36.60)
>DroYak_CAF1 31620 113 - 1
G--GGGACGGGAAUGGCGUGAAAUGCUGCUCCUUUUUUGUGAGGAGGGCGCUUAAUUUAAACGAAAUUAUUUCAUGCAACUGACGAGGGGUCUCCUUUGUGUGACAGUGUCCUUG
(--(((((.......((((((((.(((.((((((......)))))))))...((((((.....)))))))))))))).(((((((((((....)))))))....)))))))))). ( -39.00)
>consensus
G__GGGACGGGAAUCGCGUGAAAUGCUGCUCCUU_UUUGUCAGGAGGGCGCUUAAUUUAAACGAAAUUAUUUCAUGCAACUGAUGAGGGGUCUCCUUUGUGUGACAGUGUCCUUG
...((((((......((((((((.(((.(((((........))))).).)).((((((.....)))))))))))))).....(((((((....))))))).......)))))).. (-30.62 = -30.25 +  -0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:56 2006