Locus 7317

Sequence ID	3R_DroMel_CAF1
Location	19,329,025 – 19,329,160
Length	135
Max. P	0.862288

overview

Window 7

Location	19,329,025 – 19,329,133
Length	108
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	77.61
Mean single sequence MFE	-32.75
Consensus MFE	-19.30
Energy contribution	-18.28
Covariance contribution	-1.02
Combinations/Pair	1.35
Mean z-score	-1.91
Structure conservation index	0.59
SVM decision value	0.83
SVM RNA-class probability	0.862288
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19329025 108 - 27905053
GCUCAACUGUCUUGGCCCA-AUCGUGUUGCACAAUGUGUGAAAACAGGAUCAGAGUCCUGCCUAAACAUUUGUCAACCC-AGCGGCGCUUAUAUAAUCAACAAUGC---------AGAU
......((((.((((((..-...(.((((.((((.((((.....((((((....)))))).....))))))))))))).-...)))(.((....)).)..))).))---------)).. ( -23.80)
>DroPse_CAF1 144838 117 - 1
GUUCAACUGUCGAUGCUGG-GGCGUGUUGCACAAUGUGUGAAAACAGGACCAAAGUCCUGCCUAAACAUUUGUCAACCC-AGCGGCGUUUAUAUAAUCAACGAUGCCAUACCGACGGAU
......((((((..(((((-(((.....))((((.((((.....((((((....)))))).....))))))))...)))-)))((((((............))))))....)))))).. ( -41.80)
>DroGri_CAF1 134474 100 - 1
GUCCGGUUGUCCAACUG---GGCGUGUUGCACAAUGUGUGAAAACAGGAUCAAAGUCCUGCCUAAGCAUUUGUUCGCGUUUUCAGCGUUUAUGUAAUCUACA----------------U
((((((((....)))))---)))((((((((.(((((.((((((((((((....)))))......((........))))))))))))))..))))))..)).----------------. ( -30.80)
>DroMoj_CAF1 143292 100 - 1
GUCCAGUUGUCCAAGCU---GACGUGUUGCACAAUGUGUGAAAACAGGAUCAAAGUCCUGCCUAAACAUUUGUCAACGUUUUCAGCGUUUAUGUAAUCUGCA----------------U
..............(((---((..(((((.((((.((((.....((((((....)))))).....)))))))))))))...)))))....((((.....)))----------------) ( -25.20)
>DroAna_CAF1 129404 109 - 1
GCUCAACUGUCGUGGCUGGGGGCGUGUUGCACAAUGUGUGAAAACAGGAUCAGAGUCCUGCCUAAACAUUUGUCAACCC-AGCGGCGCUUAUGUAAUCAACAAUGC---------AGAU
......(((((((.((((((.((.....))((((.((((.....((((((....)))))).....))))))))...)))-))).)))....(((.....)))..))---------)).. ( -33.10)
>DroPer_CAF1 145121 117 - 1
GUUCAACUGUCGAUGCUGG-GGCGUGUUGCACAAUGUGUGAAAACAGGACCAAAGUCCUGCCUAAACAUUUGUCAACCC-AGCGGCGUUUAUAUAAUCAACGAUGCCAUACCGACGGAU
......((((((..(((((-(((.....))((((.((((.....((((((....)))))).....))))))))...)))-)))((((((............))))))....)))))).. ( -41.80)
>consensus
GUUCAACUGUCGAAGCUGG_GGCGUGUUGCACAAUGUGUGAAAACAGGAUCAAAGUCCUGCCUAAACAUUUGUCAACCC_AGCGGCGUUUAUAUAAUCAACAAUGC__________GAU
.......(((..........(((((((((.((((.((((.....((((((....)))))).....)))))))))))).......)))))..........)))................. (-19.30 = -18.28 +  -1.02)

alignment

secondary structure

dotplot

Window 8

Location	19,329,055 – 19,329,160
Length	105
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	79.99
Mean single sequence MFE	-24.78
Consensus MFE	-17.56
Energy contribution	-17.95
Covariance contribution	0.39
Combinations/Pair	1.08
Mean z-score	-1.37
Structure conservation index	0.71
SVM decision value	0.32
SVM RNA-class probability	0.685657
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19329055 105 - 27905053
UAAGUC-----UCCAAGAGACCA--AGAA-AUACGGCUCAACUGUCUUGGCCCA-AUCGUGUUGCACAAUGUGUGAAAACAGGAUCAGAGUCCUGCCUAAACAUUUGUCAACCC
...(((-----((...)))))..--....-....(((.(((.....))))))..-.....((((.((((.((((.....((((((....)))))).....)))))))))))).. ( -25.40)
>DroVir_CAF1 140699 88 - 1
UCACAUA----CACAUGAAACUA---GCUACCACUG-------------------GGCGUGUUGCACAAUGUGUGAAAACAGGAUCAAAGUCCUGCCUAAACAUUUGUCAACAU
.......----.........(((---(......)))-------------------)..((((((.((((.((((.....((((((....)))))).....)))))))))))))) ( -21.30)
>DroSim_CAF1 126510 106 - 1
UAAGUU-----UGCAAGAGACCA--AGAAAACACGGCUCAACUGUCUUGGCUCA-AUCGUGUUGCACAAUGUGUGAAAACAGGAUCAGAGUCCUGCCUAAACAUUUGUCAACCC
......-----.....(((.(((--(((.....(((.....)))))))))))).-.....((((.((((.((((.....((((((....)))))).....)))))))))))).. ( -27.40)
>DroEre_CAF1 128164 106 - 1
UAAGCC-----UCCAAGAGACCA--AGAAAACACGGCUCAACUGUCUUGGCCAA-AUCGUGUUGCACAAUGUGUGAAAACAGGAUCAGAGUCCUGCCUAAACAUUUGUCAACCC
......-----.......(.(((--(((.....(((.....))))))))).)..-.....((((.((((.((((.....((((((....)))))).....)))))))))))).. ( -22.90)
>DroYak_CAF1 130874 111 - 1
UAAGUUAAAAUAGCAAGAGACCA--AGAAAACACGGCUCAACUGUCUUGGCCCA-AUCGUGUUGCACAAUGUGUGAAAACAGGAUCAGAGUCCUGCCUAAACAUUUGUCAACCC
...(((((.((((...(((.((.--.........)))))..)))).)))))...-.....((((.((((.((((.....((((((....)))))).....)))))))))))).. ( -24.90)
>DroAna_CAF1 129434 109 - 1
UAAAUA-----AAUAAAUAAACAUUGGAGAACACAGCUCAACUGUCGUGGCUGGGGGCGUGUUGCACAAUGUGUGAAAACAGGAUCAGAGUCCUGCCUAAACAUUUGUCAACCC
......-----.((((((..((((((...(((((.((((....((....))...)))))))))...))))))((.....((((((....)))))).....))))))))...... ( -26.80)
>consensus
UAAGUU_____UACAAGAGACCA__AGAAAACACGGCUCAACUGUCUUGGCCCA_AUCGUGUUGCACAAUGUGUGAAAACAGGAUCAGAGUCCUGCCUAAACAUUUGUCAACCC
..................................(((.(((.....))))))........((((.((((.((((.....((((((....)))))).....)))))))))))).. (-17.56 = -17.95 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:00 2006