Locus 5340

Sequence ID	X_DroMel_CAF1
Location	13,928,300 – 13,928,408
Length	108
Max. P	0.963116

overview

Window 0

Location	13,928,300 – 13,928,408
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.08
Mean single sequence MFE	-31.38
Consensus MFE	-20.89
Energy contribution	-20.73
Covariance contribution	-0.16
Combinations/Pair	1.05
Mean z-score	-3.55
Structure conservation index	0.67
SVM decision value	1.55
SVM RNA-class probability	0.963116
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13928300 108 + 22224390
GCUGCAUUUGUGGGUCUUCCGCAUCCCUCUGAUUGGCCCCACAAGCUCCCCUAUA--UUC------UAUGUAUUCCUUUUUUUUUUUUUAAAGGAGUUUUGU-AGCUGC---AGCGGCAU
((((((((((((((....(((.(((.....)))))).))))))))..........--..(------((((.((((((((..........))))))))..)))-)).)))---)))..... ( -31.00)
>DroSec_CAF1 8453 101 + 1
GCUGCAUUUGUGGGUCUUCCGCAUCCCUCGGAUUG-CCCCACAAACUCCCCUAUA--UUC------UAUAUAUUCCUCUUUUUU------AAGGAGUUUUGU-AGCUGC---AGCGGCAU
((((((((((((((.(.((((.......))))..)-.))))))))..........--..(------((((.((((((.......------.))))))..)))-)).)))---)))..... ( -33.80)
>DroSim_CAF1 11335 101 + 1
GCUGCAUUUGUGGGUCUUCCGCAUCCCUCGGAUUG-CCCCACAAACUCCCCUAUA--UUC------UAUAUGCUCCUCUUUUUU------AAGGAGUUUUGU-AGCUGC---AGCGGCAU
((((((((((((((.(.((((.......))))..)-.))))))))..........--..(------((((.((((((.......------.))))))..)))-)).)))---)))..... ( -36.40)
>DroEre_CAF1 10171 106 + 1
GCUGCAUUUGUGGGUCUUCCGCAGCCCGCUGAUUG-CCCCACAAACUCCCCCAUA--UUCCACAAGUACAUAUACA--UUUUUU------AAGGAGUUUUGUUAGCUGC---AGCGGCAU
((((((...(((((.(.....(((....)))...)-.)))))(((((((......--...................--......------..))))))).......)))---)))..... ( -27.01)
>DroYak_CAF1 10051 104 + 1
GCUGCAUUUGUGGGUCUUCCGCAUCCCUCUGAUUG-CCCCACAAACUCCCCUAUAUAUUC------UAUAUAUUCC--AUUUUU------AAGGAGUUUUGU-AGCUGCAGCAGCGGCAU
((((((((((((((......(((((.....)).))-)))))))))..............(------((((.(((((--......------..)))))..)))-)).))))))........ ( -28.70)
>consensus
GCUGCAUUUGUGGGUCUUCCGCAUCCCUCUGAUUG_CCCCACAAACUCCCCUAUA__UUC______UAUAUAUUCCU_UUUUUU______AAGGAGUUUUGU_AGCUGC___AGCGGCAU
(((((..(((((((...((...........)).....)))))))(((((...........................................)))))................))))).. (-20.89 = -20.73 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	13,928,300 – 13,928,408
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.08
Mean single sequence MFE	-31.93
Consensus MFE	-20.77
Energy contribution	-21.01
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.88
Structure conservation index	0.65
SVM decision value	0.77
SVM RNA-class probability	0.846547
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13928300 108 - 22224390
AUGCCGCU---GCAGCU-ACAAAACUCCUUUAAAAAAAAAAAAAGGAAUACAUA------GAA--UAUAGGGGAGCUUGUGGGGCCAAUCAGAGGGAUGCGGAAGACCCACAAAUGCAGC
.....(((---(((...-......((((((((......................------...--..)))))))).(((((((.((.(((.....)))..))....))))))).)))))) ( -29.73)
>DroSec_CAF1 8453 101 - 1
AUGCCGCU---GCAGCU-ACAAAACUCCUU------AAAAAAGAGGAAUAUAUA------GAA--UAUAGGGGAGUUUGUGGGG-CAAUCCGAGGGAUGCGGAAGACCCACAAAUGCAGC
.....(((---(((...-...(((((((((------..................------...--....)))))))))(((((.-...((((.......))))...)))))...)))))) ( -31.11)
>DroSim_CAF1 11335 101 - 1
AUGCCGCU---GCAGCU-ACAAAACUCCUU------AAAAAAGAGGAGCAUAUA------GAA--UAUAGGGGAGUUUGUGGGG-CAAUCCGAGGGAUGCGGAAGACCCACAAAUGCAGC
.....(((---((..((-(.....((((((------......))))))....))------)..--.........(((((((((.-...((((.......))))...)))))))))))))) ( -33.70)
>DroEre_CAF1 10171 106 - 1
AUGCCGCU---GCAGCUAACAAAACUCCUU------AAAAAA--UGUAUAUGUACUUGUGGAA--UAUGGGGGAGUUUGUGGGG-CAAUCAGCGGGCUGCGGAAGACCCACAAAUGCAGC
...(((((---(..(((.(((((.((((((------......--(.((((......)))).).--....)))))))))))..))-)...))))))((((((.............)))))) ( -33.62)
>DroYak_CAF1 10051 104 - 1
AUGCCGCUGCUGCAGCU-ACAAAACUCCUU------AAAAAU--GGAAUAUAUA------GAAUAUAUAGGGGAGUUUGUGGGG-CAAUCAGAGGGAUGCGGAAGACCCACAAAUGCAGC
.....((((((((..((-(((((.((((((------......--....((((((------...))))))))))))))))))).)-))......(((...(....).)))......))))) ( -31.50)
>consensus
AUGCCGCU___GCAGCU_ACAAAACUCCUU______AAAAAA_AGGAAUAUAUA______GAA__UAUAGGGGAGUUUGUGGGG_CAAUCAGAGGGAUGCGGAAGACCCACAAAUGCAGC
.(((.(((.....)))........(((((.......................................))))).(((((((((....(((.....))).(....).)))))))))))).. (-20.77 = -21.01 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:24 2006