Locus 2032

Sequence ID	2R_DroMel_CAF1
Location	7,677,027 – 7,677,241
Length	214
Max. P	0.901647

overview

Window 1

Location	7,677,027 – 7,677,136
Length	109
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	73.41
Mean single sequence MFE	-24.90
Consensus MFE	-17.54
Energy contribution	-17.21
Covariance contribution	-0.33
Combinations/Pair	1.41
Mean z-score	-0.84
Structure conservation index	0.70
SVM decision value	0.04
SVM RNA-class probability	0.555390
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7677027 109 - 20766785
GCUCCCAGG-UUACUGCCAAAUUUGCGAUAAA------ACGGGAGCUGCAAUGA-AUAUGUUCGUGGCGAUUGUUAAGAAUUAAUCGUGACUGCUGAUAGUUGCAUACAUAUAAACU---
((((((...-(((.(((.......))).))).------..))))))((((((..-....((..((.(((((((........))))))).)).)).....))))))............--- ( -30.80)
>DroPse_CAF1 5616 108 - 1
ACUCCCAGC-UUACUACUAAUUUAGCGAUUA-------AAGGGAGUUGCAAUGA-AUAUGUUCGUGAUGAUUGAACAGCAUAAAUCGUUGCUGCUGAUACUUGCAUACACUGGAAAA---
((((((.((-(............))).....-------..)))))).(((((((-...((((((.......)))))).......)))))))(((........)))............--- ( -22.60)
>DroGri_CAF1 7732 118 - 1
ACGCCCAAC-UUACUACCAAUUUAGCGAUUGUUUCCUUUUGGGAAGUGCAAUGU-GAAUGUUCGUUACGAUUUUCUAGACUAAAUCGCGACUGCUGAUAGUUGCAUACAAGCAUAGUUCU
.(((...((-((....((((...((.((.....)))).)))).)))).....))-).(((((.((...(((((........)))))(((((((....)))))))..)).)))))...... ( -22.60)
>DroWil_CAF1 6652 110 - 1
ACUCCCAAGUUUACUACCAAUUUAGCGAUAAUGG---UGAGGGAGAUGCAAUGAGAAAUGUUCGUUAUGAUUGCAAAGACUAAGUCAUAACUGCUGAUAGUUGCAGACA----AACU---
.(((((.((....))((((..(((....))))))---)..))))).((((((.......((..(((((((((..........))))))))).)).....))))))....----....--- ( -25.60)
>DroMoj_CAF1 7924 116 - 1
ACGCCCAAU-UUACUACCAAUUUAGCGAUUGUCUUCGAAUGGGCGGUGCAAUGU-AAAUGUUCGUUAUGAUUUUGUAGACUAAAUUUUAACUGCUGAUAGUUGCAUACAAACAUAAAC--
.((((((..-...(((......)))(((......)))..))))))(((((((..-....((..((((.(((((........))))).)))).)).....)))))))............-- ( -25.20)
>DroPer_CAF1 5617 108 - 1
ACUCCCAGC-UUACUACUAAUUUAGCGAUUA-------AAGGGAGUUGCAAUGA-AUAUGUUCGUGAUGAUUGAACAGCAUAAAUCGUUGCUGCUGAUACUUGCAUACACUGGAACA---
((((((.((-(............))).....-------..)))))).(((((((-...((((((.......)))))).......)))))))(((........)))............--- ( -22.60)
>consensus
ACUCCCAAC_UUACUACCAAUUUAGCGAUUAU______AAGGGAGGUGCAAUGA_AAAUGUUCGUGAUGAUUGUAAAGAAUAAAUCGUAACUGCUGAUAGUUGCAUACAAACAAACA___
.(((((..................................))))).((((((.......((..(((((((((..........))))))))).)).....))))))............... (-17.54 = -17.21 +  -0.33)

alignment

secondary structure

dotplot

Window 2

Location	7,677,136 – 7,677,241
Length	105
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	80.51
Mean single sequence MFE	-23.40
Consensus MFE	-19.98
Energy contribution	-19.32
Covariance contribution	-0.66
Combinations/Pair	1.38
Mean z-score	-1.88
Structure conservation index	0.85
SVM decision value	1.02
SVM RNA-class probability	0.901647
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7677136 105 - 20766785
AUUCUU-CAAAAAUUACCAUUCUAAAAUCUUAUUUACGUGGUUAGAAACGUUUCCAAGUGAUCAGCCUCUCUGGAAAUGCUUCAUGCCGCGUUAGAAAAACGACGA
......-............(((((...........(((((((..(((.((((((((.(.((......)).))))))))).)))..))))))))))))......... ( -23.90)
>DroVir_CAF1 6898 104 - 1
AUCUUUACGAUUGUAUAUGUAGUUAGAU-AUAUUUACAUGGC-CGUAGAGUUCCCAGUUGUACGCAUAUACUGGUAACGCUUCAUGCCAUGUUAGAUCAAACAAUA
.....................(((.(((-......(((((((-...((.(((.(((((((....))...))))).))).))....)))))))...))).))).... ( -23.80)
>DroSec_CAF1 6852 105 - 1
AUUCUU-CGAAAAUUACCAUUCUAAAAUCUUAUUUACGUGGUUAGAAACGUUUCCAAGUGAACAGCCUCUCUGGAAAUGCUUCAUGCCGCGUUAGAAAAACGACGA
..((.(-((....(((......)))..(((.....(((((((..(((.((((((((.(.((......)).))))))))).)))..))))))).)))....))).)) ( -24.30)
>DroSim_CAF1 6540 105 - 1
AUUAUU-CAAAAAUUACCAUUCUAAAAUCUUAUUUACGUGGUUAGAAACGUUUCCAAGUGAACAGCCUCUCUGGAAAUGCUUCAUGCCGCGUUAGAAAAACGACGA
......-............(((((...........(((((((..(((.((((((((.(.((......)).))))))))).)))..))))))))))))......... ( -24.10)
>DroEre_CAF1 6856 105 - 1
AUUCCU-CCAAUAUGAUUAUUCUAACAUCUUAUUUACGUGGUCAAGAACGUUUCCAAGUGAACAGCCUCUCUGGAAAUGCUUCAUGCCGCGUUAGAAAAACGACGA
......-............(((((...........((((((.((.(((((((((((.(.((......)).))))))))).))).)))))))))))))......... ( -23.90)
>DroYak_CAF1 6843 105 - 1
AUUCCU-CCAAAAUUAUUAUUCUAAAAUACUAUUUACGUGGUCAGAAACGUUUCUAAGUGAACAGCCUCUCUGGAAAUGCUUCAUGCCGCGUCAGAAAAACGACGA
......-.........................((((((((((..(((.((((((((.(.((......)).))))))))).)))..))))))).))).......... ( -20.40)
>consensus
AUUCUU_CAAAAAUUACCAUUCUAAAAUCUUAUUUACGUGGUUAGAAACGUUUCCAAGUGAACAGCCUCUCUGGAAAUGCUUCAUGCCGCGUUAGAAAAACGACGA
................................((((((((((..(((.(((((((.((.((......)).))))))))).)))..))))))).))).......... (-19.98 = -19.32 +  -0.66)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:22 2006