Locus 8144

Sequence ID	3R_DroMel_CAF1
Location	21,893,006 – 21,893,108
Length	102
Max. P	0.909142

overview

Window 8

Location	21,893,006 – 21,893,108
Length	102
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	75.96
Mean single sequence MFE	-32.15
Consensus MFE	-21.05
Energy contribution	-21.55
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.65
SVM decision value	1.06
SVM RNA-class probability	0.909142
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21893006 102 + 27905053
GGUCUCCGG-UUGUCGGCUCUCUUUGGCGGCUGCUU------UGGCCAAAUCAAUUGAGCCGCCUUCCCCCAUAAACGAGCCAAAACAAAUG--ACUCCGACUUG---CCUCGA
((((....(-((...(((((.....(((((((...(------(((.....))))...))))))).............)))))..)))....)--))).(((....---..))). ( -27.97)
>DroVir_CAF1 8295 82 + 1
CGUC----G-UCGGCGGCU-GCUUUGGCGGCUGCUU------UGGCCAAAUCAAUUGAGCCGCCUGC------AAACGAGCCAAAACAAAUGAGACUUG--------------A
.(((----.-(((((((((-((....))((((....------.))))..........))))))).((------......))..........)))))...--------------. ( -26.80)
>DroPse_CAF1 7717 106 + 1
GGUCUUGGUUUUGGCGGCUCUCUUUGGCGGCUGCUU------UGGCCAAAUCAAUUGAGCCGCCUUCCCCCAUAAACGAGCCAAAACAAAUG--ACUUGGCCUGGCUGGCACAA
.(((.(((....((((((((...((((.((((....------.))))...))))..)))))))).....)))......(((((...(((...--..)))...)))))))).... ( -37.30)
>DroGri_CAF1 8101 80 + 1
CGUC----G-ACGGCGGCU-GCUUUGGCGGCUGCUU------UGGCCAAAUCAAUUGAGCCGCCUGC------AAACGAGCCAAAACAAAUG--ACUUG--------------A
.(((----(-..(((((((-((....))((((....------.))))..........))))))).((------......)).........))--))...--------------. ( -26.40)
>DroAna_CAF1 7499 97 + 1
GGAUGGCGG-CUGGCGGCUCUCUUUGGCGGCUGCUUUGGCUUUGGCCAAAUCAAUUGAGCCGCCUUCCUCCAUAAACGAGCUAAAACAAAUG--ACUCCA--------------
..((((.((-..((((((((..((((((.(..((....))..).))))))......))))))))..)).))))....((((..........)--.)))..-------------- ( -37.10)
>DroPer_CAF1 7638 106 + 1
GGUCUUGGUUUUGGCGGCUCUCUUUGGCGGCUGCUU------UGGCCAAAUCAAUUGAGCCGCCUUCCCCCAUAAACGAGCCAAAACAAAUG--ACUUGGCCUGGCUGGCACAA
.(((.(((....((((((((...((((.((((....------.))))...))))..)))))))).....)))......(((((...(((...--..)))...)))))))).... ( -37.30)
>consensus
GGUCU__GG_UUGGCGGCUCUCUUUGGCGGCUGCUU______UGGCCAAAUCAAUUGAGCCGCCUUCCCCCAUAAACGAGCCAAAACAAAUG__ACUUGG_____________A
............((((((((...((((.((((...........))))...))))..)))))))).................................................. (-21.05 = -21.55 +   0.50)

alignment

secondary structure

dotplot

Window 9

Location	21,893,006 – 21,893,108
Length	102
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	75.96
Mean single sequence MFE	-32.88
Consensus MFE	-20.07
Energy contribution	-20.57
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.46
Structure conservation index	0.61
SVM decision value	0.33
SVM RNA-class probability	0.692903
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21893006 102 - 27905053
UCGAGG---CAAGUCGGAGU--CAUUUGUUUUGGCUCGUUUAUGGGGGAAGGCGGCUCAAUUGAUUUGGCCA------AAGCAGCCGCCAAAGAGAGCCGACAA-CCGGAGACC
((((..---....)))).((--(.(..((((((((((.(((.(((.((...(((((.(((.....)))))).------..))..)).))).)))))))))).))-)..).))). ( -33.40)
>DroVir_CAF1 8295 82 - 1
U--------------CAAGUCUCAUUUGUUUUGGCUCGUUU------GCAGGCGGCUCAAUUGAUUUGGCCA------AAGCAGCCGCCAAAGC-AGCCGCCGA-C----GACG
.--------------..........(((((.(((((.((((------...((((((((((.....)))((..------..))))))))).))))-)))))..))-)----)).. ( -26.50)
>DroPse_CAF1 7717 106 - 1
UUGUGCCAGCCAGGCCAAGU--CAUUUGUUUUGGCUCGUUUAUGGGGGAAGGCGGCUCAAUUGAUUUGGCCA------AAGCAGCCGCCAAAGAGAGCCGCCAAAACCAAGACC
(((.(((.....))))))..--.....(((((((((((....))))....((((((((......((((((..------........))))))..))))))))....))))))). ( -37.40)
>DroGri_CAF1 8101 80 - 1
U--------------CAAGU--CAUUUGUUUUGGCUCGUUU------GCAGGCGGCUCAAUUGAUUUGGCCA------AAGCAGCCGCCAAAGC-AGCCGCCGU-C----GACG
.--------------..(((--((.......)))))((((.------((.(((((((.......((((((..------........))))))..-)))))))))-.----)))) ( -26.40)
>DroAna_CAF1 7499 97 - 1
--------------UGGAGU--CAUUUGUUUUAGCUCGUUUAUGGAGGAAGGCGGCUCAAUUGAUUUGGCCAAAGCCAAAGCAGCCGCCAAAGAGAGCCGCCAG-CCGCCAUCC
--------------..(((.--.(.......)..)))....((((.((..((((((((......((((((....))))))((....))......))))))))..-)).)))).. ( -36.20)
>DroPer_CAF1 7638 106 - 1
UUGUGCCAGCCAGGCCAAGU--CAUUUGUUUUGGCUCGUUUAUGGGGGAAGGCGGCUCAAUUGAUUUGGCCA------AAGCAGCCGCCAAAGAGAGCCGCCAAAACCAAGACC
(((.(((.....))))))..--.....(((((((((((....))))....((((((((......((((((..------........))))))..))))))))....))))))). ( -37.40)
>consensus
U_____________CCAAGU__CAUUUGUUUUGGCUCGUUUAUGGGGGAAGGCGGCUCAAUUGAUUUGGCCA______AAGCAGCCGCCAAAGAGAGCCGCCAA_CC__AGACC
..................................................((((((((......((((((................))))))..))))))))............ (-20.07 = -20.57 +   0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:03:35 2006