Locus 3954

Sequence ID	2R_DroMel_CAF1
Location	13,047,388 – 13,047,516
Length	128
Max. P	0.931200

overview

Window 3

Location	13,047,388 – 13,047,482
Length	94
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	79.10
Mean single sequence MFE	-29.27
Consensus MFE	-18.68
Energy contribution	-19.57
Covariance contribution	0.89
Combinations/Pair	1.21
Mean z-score	-1.93
Structure conservation index	0.64
SVM decision value	0.87
SVM RNA-class probability	0.870444
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13047388 94 - 20766785
AAAAGAGUUUGGG----------------GGGGAAAACAAAGGAAGCCGGCUGGCGUUUGGCGGCGCACGCCAAGCCAAACACGACCGAGUUUAUCGAACUCAUAUUGAA
....((((((((.----------------.(......).....(((((((.(.(.((((((((((....)))..))))))).).)))).)))).))))))))........ ( -31.10)
>DroSec_CAF1 17817 94 - 1
AAAAGAGUUUGGG----------------GGGAAAAACAAAGGAAGCCGGCUGGCGGUUGGCGGCGCACGCCAAGCCAAACACGAGCGAGUUUAUCGAACUCAUAUUGAA
....((((((((.----------------.(......).....((((..(((.(.(.((((((((....)))..))))).).).)))..)))).))))))))........ ( -27.90)
>DroSim_CAF1 17557 96 - 1
AAAAGAGUUUGGGGG--------------GGGAAAAACAAAGGAAGCCGGCUGGCGGUUGGCGGCGCACGCCAAGCCAAACACGAGCGAGUUUAUCGAACUCAUAUUGAA
....((((((((...--------------.(......).....((((..(((.(.(.((((((((....)))..))))).).).)))..)))).))))))))........ ( -27.90)
>DroEre_CAF1 19543 103 - 1
GAAAGAGUUUGGUGGGGAGCGAGGGGGAGGGGGGAAACAAAGAAAGGCGGC-------UGGCGGCGCACGCCAAGCCAAACACGAGCGAGUUUAUCGAACUCAUAUUGAA
....((((((((((((..((..(.........(....)..........(((-------(((((.....)))).)))).....)..))...))))))))))))........ ( -33.00)
>DroYak_CAF1 20122 96 - 1
AAAAGAGUUUGGGGGGGA--------------AAAAACAAAGGAAGGCGGCUGCCGGCUGACGGCGCACGCCAAGCCAAACACGAGCGAGUUUAUCGAACUCAUAUUGAA
....((((((((......--------------.........((..((((((.((((.....)))))).))))...))((((.(....).)))).))))))))........ ( -30.70)
>DroPer_CAF1 21921 96 - 1
AAAACAAUAGGAUGGGGA--------------AGAGGAAGGGGCACGUGGUCGGAGACUGUCGGCGCACGCCAAGCCAAACGCGAGCGGGUUUAUCGAACUCAUAUUGAA
....(((((...((((..--------------.((......(((..((((((((......))))).))))))(((((...(....)..))))).))...))))))))).. ( -25.00)
>consensus
AAAAGAGUUUGGGGG______________GGGAAAAACAAAGGAAGCCGGCUGGCGGUUGGCGGCGCACGCCAAGCCAAACACGAGCGAGUUUAUCGAACUCAUAUUGAA
......((((((.................................((((((.....))))))(((....)))...)))))).(((..((((((...))))))...))).. (-18.68 = -19.57 +   0.89)

alignment

secondary structure

dotplot

Window 4

Location	13,047,425 – 13,047,516
Length	91
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	71.58
Mean single sequence MFE	-37.35
Consensus MFE	-12.59
Energy contribution	-14.53
Covariance contribution	1.95
Combinations/Pair	1.28
Mean z-score	-2.35
Structure conservation index	0.34
SVM decision value	1.21
SVM RNA-class probability	0.931200
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13047425 91 - 20766785
CUACCCAGC-----CACUCCCUUCCUGGCCCCAAAAUCCAAAAGAGUUUGGG----------------GGGGAAAACAAAGGAAGCCGGCUGGCGUUUGGCGGCGCACGCCA
..(((((((-----(.((.(((((((..(((((((.((.....)).))))))----------------)))))......))).))..)))))).)).(((((.....))))) ( -37.10)
>DroSec_CAF1 17854 91 - 1
CUACACAGC-----CACUCCCUUCCUGGCCCCAAAAUCCAAAAGAGUUUGGG----------------GGGAAAAACAAAGGAAGCCGGCUGGCGGUUGGCGGCGCACGCCA
.......((-----((((..((((((..(((((((.((.....)).))))))----------------)(......)..))))))..)).))))...(((((.....))))) ( -33.80)
>DroSim_CAF1 17594 93 - 1
CUACCCAGC-----CACUCCCUUCCUGGCCCCAAAAUCCAAAAGAGUUUGGGGG--------------GGGAAAAACAAAGGAAGCCGGCUGGCGGUUGGCGGCGCACGCCA
...((((((-----(.....((((((..((((....((((((....)))))).)--------------)))........))))))..)))))).)..(((((.....))))) ( -37.80)
>DroEre_CAF1 19580 100 - 1
CUACCCAGC-----CACUCCCUUCCUGGCCCCAAAAUCCGAAAGAGUUUGGUGGGGAGCGAGGGGGAGGGGGGAAACAAAGAAAGGCGGC-------UGGCGGCGCACGCCA
....(((((-----(.((((((((((.(((((.(((..(....)..)))....))).)).)))))).))))(....)..........)))-------))).(((....))). ( -47.30)
>DroYak_CAF1 20159 93 - 1
CUACCCAGC-----CACUCCCUGCCUGGCCCCAAAAUCCAAAAGAGUUUGGGGGGGA--------------AAAAACAAAGGAAGGCGGCUGCCGGCUGACGGCGCACGCCA
...(((.((-----((.........))))((((((.((.....)).)))))))))..--------------.............((((((.((((.....)))))).)))). ( -35.70)
>DroPer_CAF1 21958 88 - 1
GCAG-CAGGCAUGGCAUUCCUUUCCC--UCCC-------AAAACAAUAGGAUGGGGA--------------AGAGGAAGGGGCACGUGGUCGGAGACUGUCGGCGCACGCCA
((..-...)).((((..(((((((((--((((-------....(....)....))).--------------)).))))))))...((((((((......))))).))))))) ( -32.40)
>consensus
CUACCCAGC_____CACUCCCUUCCUGGCCCCAAAAUCCAAAAGAGUUUGGGGG______________GGGAAAAACAAAGGAAGCCGGCUGGCGGUUGGCGGCGCACGCCA
............................(((((((.((.....)).)))))))...............................((((((.....))))))(((....))). (-12.59 = -14.53 +   1.95)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:08:12 2006