Locus 6159

Sequence ID	2R_DroMel_CAF1
Location	19,375,903 – 19,376,027
Length	124
Max. P	0.973601

overview

Window 0

Location	19,375,903 – 19,376,007
Length	104
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	90.99
Mean single sequence MFE	-34.25
Consensus MFE	-30.31
Energy contribution	-30.53
Covariance contribution	0.22
Combinations/Pair	1.07
Mean z-score	-2.17
Structure conservation index	0.88
SVM decision value	1.71
SVM RNA-class probability	0.973601
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19375903 104 - 20766785
CAGUUGGACUUUGGCUCUGAUAAUUCAUAACGAUUUGUGGCAGCAGCAGCCGAUUGAAUCUGAAAGGGCCAAAGUCCAAACUCGA-AUUCGCAGUGACGUCUUGC
...(((((((((((((((((....)).....(((((.((((.......))))...)))))....)))))))))))))))(((((.-...)).))).......... ( -35.50)
>DroSec_CAF1 2784 104 - 1
CGGUUGGACUUUGGCUCUGAUAAUUCAUAACGAUUUGUGGCAGCAGCAGCCGAUUGAAGCUGAAAGGGCCAAAGUCCAAACUCGA-AUUCGCAGUGACGUCUUGC
((.(((((((((((((((......((((((....))))))((((..(((....)))..))))..)))))))))))))))(((((.-...)).)))..))...... ( -35.60)
>DroSim_CAF1 2835 104 - 1
CGGUUGGACUUUGGCUCUGAUAAUUCAUAACGAUUUGUGGCAGCAGCAGCCGAUUGAAUCUGAAAGGGCCAAAGUCCAAACUCGA-AUUCGCAGUGACGUCUUGC
((.(((((((((((((((((....)).....(((((.((((.......))))...)))))....)))))))))))))))(((((.-...)).)))..))...... ( -35.70)
>DroEre_CAF1 3056 104 - 1
CGGUUGGACUUUGGCUCUGAUAAUUCAUAACGAUUUGUGGCAGCAGCAGCCGAUUGAAUCCGAAAGGGCCAAAGUCCAAACUCGA-GUUCGCAGUGACGUCUUGC
((.(((((((((((((((((....)).....(((((.((((.......))))...)))))....)))))))))))))))(((((.-...)).)))..))...... ( -35.30)
>DroYak_CAF1 2840 104 - 1
CGGUUGGACUUUGGCUCUGACAAUUCAUAACGAUUUGUGGCAGCAGCAGCCGAUUGAAUCUGAAAGGGCCAAAGUCCAAACUCGA-GUUCGCAGUGACGUCUUGC
((.(((((((((((((((..(((((((..........((((.......))))..))))).))..)))))))))))))))(((((.-...)).)))..))...... ( -35.30)
>DroAna_CAF1 2152 92 - 1
CGGUUGGACUUUGCCUUCAUCAAU---------UUUGUGGCAUCAGCGGCCGAUUGAAUCUCA-AGGGCCAAAGUCCAAACUCGAAAUUCGCAGUGACGUCU---
((.((((((((((((..((.....---------..)).)))......((((..(((.....))-).)))))))))))))(((((.....)).)))..))...--- ( -28.10)
>consensus
CGGUUGGACUUUGGCUCUGAUAAUUCAUAACGAUUUGUGGCAGCAGCAGCCGAUUGAAUCUGAAAGGGCCAAAGUCCAAACUCGA_AUUCGCAGUGACGUCUUGC
...(((((((((((((((.((((.((.....)).))))(((.......))).............)))))))))))))))(((((.....)).))).......... (-30.31 = -30.53 +   0.22)

alignment

secondary structure

dotplot

Window 1

Location	19,375,928 – 19,376,027
Length	99
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	84.72
Mean single sequence MFE	-30.36
Consensus MFE	-23.74
Energy contribution	-24.63
Covariance contribution	0.89
Combinations/Pair	1.14
Mean z-score	-1.98
Structure conservation index	0.78
SVM decision value	0.26
SVM RNA-class probability	0.656948
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19375928 99 + 20766785
UUGGACUUUGGCCCUUUCAGAUUCAAUCGGCUGCUGCUGCCACAAAUCGUUAUGAAUUAUCAGAGCCAAAGUCCAACUGGUG--CAGCCCGUGUUUGGAAU--
.(((((((((((.((....((((((...(((.......)))((.....))..))))))...)).)))))))))))((.((..--...)).)).........-- ( -29.70)
>DroSec_CAF1 2809 99 + 1
UUGGACUUUGGCCCUUUCAGCUUCAAUCGGCUGCUGCUGCCACAAAUCGUUAUGAAUUAUCAGAGCCAAAGUCCAACCGGUG--CAGCCCGUGUCUGGAAU--
((((((((((((.((......((((...(((.......)))((.....))..)))).....)).))))))))))))((((.(--((.....)))))))...-- ( -30.40)
>DroSim_CAF1 2860 99 + 1
UUGGACUUUGGCCCUUUCAGAUUCAAUCGGCUGCUGCUGCCACAAAUCGUUAUGAAUUAUCAGAGCCAAAGUCCAACCGGUG--CAGCCCGUGUCUGGAAU--
((((((((((((.((....((((((...(((.......)))((.....))..))))))...)).))))))))))))((((.(--((.....)))))))...-- ( -33.20)
>DroEre_CAF1 3081 99 + 1
UUGGACUUUGGCCCUUUCGGAUUCAAUCGGCUGCUGCUGCCACAAAUCGUUAUGAAUUAUCAGAGCCAAAGUCCAACCGGUG--CAGCCCACGUUUAGGAU--
((((((((((((.((....((((((...(((.......)))((.....))..))))))...)).))))))))))))((...(--(.......))...))..-- ( -31.10)
>DroYak_CAF1 2865 99 + 1
UUGGACUUUGGCCCUUUCAGAUUCAAUCGGCUGCUGCUGCCACAAAUCGUUAUGAAUUGUCAGAGCCAAAGUCCAACCGGUG--CAGUAUAGCUUUGGGAU--
((((((((((((.((....((((((...(((.......)))((.....))..))))))...)).))))))))))))((((.(--(......)).))))...-- ( -34.40)
>DroAna_CAF1 2175 91 + 1
UUGGACUUUGGCCCU-UGAGAUUCAAUCGGCCGCUGAUGCCACAAA---------AUUGAUGAAGGCAAAGUCCAACCGGCAUACAGUU--AGUCAAGCAUAA
(((((((((((((.(-((.....)))..))))......(((.....---------.........))))))))))))..(((........--.)))........ ( -23.34)
>consensus
UUGGACUUUGGCCCUUUCAGAUUCAAUCGGCUGCUGCUGCCACAAAUCGUUAUGAAUUAUCAGAGCCAAAGUCCAACCGGUG__CAGCCCGUGUCUGGAAU__
((((((((((((.((....((((((...(((.......)))((.....))..))))))...)).))))))))))))..(((.....))).............. (-23.74 = -24.63 +   0.89)

alignment

secondary structure

dotplot

Window 2

Location	19,375,928 – 19,376,027
Length	99
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	84.72
Mean single sequence MFE	-34.17
Consensus MFE	-28.00
Energy contribution	-27.87
Covariance contribution	-0.14
Combinations/Pair	1.15
Mean z-score	-2.93
Structure conservation index	0.82
SVM decision value	1.25
SVM RNA-class probability	0.936461
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19375928 99 - 20766785
--AUUCCAAACACGGGCUG--CACCAGUUGGACUUUGGCUCUGAUAAUUCAUAACGAUUUGUGGCAGCAGCAGCCGAUUGAAUCUGAAAGGGCCAAAGUCCAA
--...........((....--..))..(((((((((((((((((....)).....(((((.((((.......))))...)))))....))))))))))))))) ( -34.70)
>DroSec_CAF1 2809 99 - 1
--AUUCCAGACACGGGCUG--CACCGGUUGGACUUUGGCUCUGAUAAUUCAUAACGAUUUGUGGCAGCAGCAGCCGAUUGAAGCUGAAAGGGCCAAAGUCCAA
--......(((.(((....--..))))))(((((((((((((......((((((....))))))((((..(((....)))..))))..))))))))))))).. ( -37.50)
>DroSim_CAF1 2860 99 - 1
--AUUCCAGACACGGGCUG--CACCGGUUGGACUUUGGCUCUGAUAAUUCAUAACGAUUUGUGGCAGCAGCAGCCGAUUGAAUCUGAAAGGGCCAAAGUCCAA
--......(((.(((....--..))))))(((((((((((((((....)).....(((((.((((.......))))...)))))....))))))))))))).. ( -37.60)
>DroEre_CAF1 3081 99 - 1
--AUCCUAAACGUGGGCUG--CACCGGUUGGACUUUGGCUCUGAUAAUUCAUAACGAUUUGUGGCAGCAGCAGCCGAUUGAAUCCGAAAGGGCCAAAGUCCAA
--......(((.(((....--..))))))(((((((((((((((....)).....(((((.((((.......))))...)))))....))))))))))))).. ( -34.60)
>DroYak_CAF1 2865 99 - 1
--AUCCCAAAGCUAUACUG--CACCGGUUGGACUUUGGCUCUGACAAUUCAUAACGAUUUGUGGCAGCAGCAGCCGAUUGAAUCUGAAAGGGCCAAAGUCCAA
--...((...((......)--)...))(((((((((((((((..(((((((..........((((.......))))..))))).))..))))))))))))))) ( -34.20)
>DroAna_CAF1 2175 91 - 1
UUAUGCUUGACU--AACUGUAUGCCGGUUGGACUUUGCCUUCAUCAAU---------UUUGUGGCAUCAGCGGCCGAUUGAAUCUCA-AGGGCCAAAGUCCAA
....((...((.--....))..))...((((((((((((..((.....---------..)).)))......((((..(((.....))-).))))))))))))) ( -26.40)
>consensus
__AUUCCAAACACGGGCUG__CACCGGUUGGACUUUGGCUCUGAUAAUUCAUAACGAUUUGUGGCAGCAGCAGCCGAUUGAAUCUGAAAGGGCCAAAGUCCAA
...............((((.....))))((((((((((((((.((((.((.....)).))))(((.......))).............)))))))))))))). (-28.00 = -27.87 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:22 2006