Locus 4643

Sequence ID	3L_DroMel_CAF1
Location	13,182,799 – 13,183,027
Length	228
Max. P	0.999924

overview

Window 8

Location	13,182,799 – 13,182,919
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.33
Mean single sequence MFE	-36.68
Consensus MFE	-34.10
Energy contribution	-33.94
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.28
Structure conservation index	0.93
SVM decision value	0.45
SVM RNA-class probability	0.740025
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13182799 120 + 23771897
UCAACGCCCGGCGUCAUCUGCGGCCUUUAUCAAUUCACCUUCCUUUGGCGAGCCUCCUCUUCUGGCUGUUUACAUAACCAAGGCGGCAUGCCACUUUAGUGGGCGUGCUGCAAAACGUAA
...(((...((........((((((........(((.((.......)).)))...........))))))........))...((((((((((((....)).))))))))))....))).. ( -34.70)
>DroSec_CAF1 34363 120 + 1
UCAACGCCCGGCGUCAUCUGCGGCCUUUAUCAAUUCACCUUCCUUUGGCGAGCCUCCUCUUCUGGCUGUUUACAUAACCAAGGCGGCGUGCCACUUUAGUGGGCGUGCUGCAAAACGUAA
...(((((((((((.....)).)))....................(((((.(((.(((....(((.(((....))).)))))).))).))))).......)))))).............. ( -33.90)
>DroSim_CAF1 32599 120 + 1
UCAACGCCCGGCGUCAUCUGCGGCCUUUAUCAAUUCACCUUCCUUUGGCGAGCCUCCUCUUCUGGCUGUUUACAUAACCAAGGCGGCAUGCCACUUUAGUGGGCGUGCUGCAAAACGUAA
...(((...((........((((((........(((.((.......)).)))...........))))))........))...((((((((((((....)).))))))))))....))).. ( -34.70)
>DroEre_CAF1 37880 119 + 1
UCAACGCCCGGCGUCAUCUGCGGCCUUUAUCAAUUCGCCUUCCUUUGGCGAGCCUCCUCUGCUGGCUGUUUACAUAACCAAGGCGGCAUGCCACUUUAGUGGGCGUGCUGCAA-AGGUAA
..((((.((((((((......))).........((((((.......))))))........))))).))))......(((...((((((((((((....)).))))))))))..-.))).. ( -43.90)
>DroYak_CAF1 33581 120 + 1
UCAACGCCCGGCGUCAUCUGCGGCCUUUAUCAAUUCACCUUCCUUUGGAGAGCCUCCUCUUCUGGCUGUUUACAUAACCAAGGCGGCAUGCCACUUUAGUGGGCGUGCCACAAAACGUAA
...((((...))))....(((((((((..............((...((((((....)))))).))..............)))))((((((((((....)).))))))))......)))). ( -36.19)
>consensus
UCAACGCCCGGCGUCAUCUGCGGCCUUUAUCAAUUCACCUUCCUUUGGCGAGCCUCCUCUUCUGGCUGUUUACAUAACCAAGGCGGCAUGCCACUUUAGUGGGCGUGCUGCAAAACGUAA
...((((((((((.....(((.(((((.......((.((.......)).))(((.........))).............))))).)))))))((....)))))))).............. (-34.10 = -33.94 +  -0.16)

alignment

secondary structure

dotplot

Window 9

Location	13,182,839 – 13,182,957
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.55
Mean single sequence MFE	-28.98
Consensus MFE	-25.66
Energy contribution	-25.54
Covariance contribution	-0.12
Combinations/Pair	1.09
Mean z-score	-1.97
Structure conservation index	0.89
SVM decision value	2.45
SVM RNA-class probability	0.994075
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13182839 118 + 23771897
UCCUUUGGCGAGCCUCCUCUUCUGGCUGUUUACAUAACCAAGGCGGCAUGCCACUUUAGUGGGCGUGCUGCAAAACGUAAAAGAAGAAAAUACUAUUAAUAAGAAAAAAUAAGAA--AAA
..((((.(((((((.........))))...............((((((((((((....)).))))))))))....))).))))................................--... ( -30.70)
>DroSec_CAF1 34403 117 + 1
UCCUUUGGCGAGCCUCCUCUUCUGGCUGUUUACAUAACCAAGGCGGCGUGCCACUUUAGUGGGCGUGCUGCAAAACGUAAAAGAAGAAAAUACUAUUAAUA-CAAAAAAUAAGAA--AAA
..((((.(((((((.........))))...............((((((((((((....)).))))))))))....))).))))..................-.............--... ( -27.30)
>DroSim_CAF1 32639 117 + 1
UCCUUUGGCGAGCCUCCUCUUCUGGCUGUUUACAUAACCAAGGCGGCAUGCCACUUUAGUGGGCGUGCUGCAAAACGUAAAAUAAGAAAAUACUAUUAAUA-CAAAAAAUAAGAA--AAG
..(((..(((((((.........))))...............((((((((((((....)).))))))))))....))).....)))...............-.............--... ( -28.20)
>DroEre_CAF1 37920 115 + 1
UCCUUUGGCGAGCCUCCUCUGCUGGCUGUUUACAUAACCAAGGCGGCAUGCCACUUUAGUGGGCGUGCUGCAA-AGGUAAAA---GAAAAUACUAUUAAUA-CAAAAAAUAAGAAACAAA
..(((((((.(((.......))).))).........(((...((((((((((((....)).))))))))))..-.))).)))---)...............-.................. ( -32.10)
>DroYak_CAF1 33621 114 + 1
UCCUUUGGAGAGCCUCCUCUUCUGGCUGUUUACAUAACCAAGGCGGCAUGCCACUUUAGUGGGCGUGCCACAAAACGUAAAA---GAAAAUACUAUUAAUG-CAAAAAAUGAGAA--AAA
..((((((..((((.........))))(....)....)))))).((((((((((....)).)))))))).............---................-.............--... ( -26.60)
>consensus
UCCUUUGGCGAGCCUCCUCUUCUGGCUGUUUACAUAACCAAGGCGGCAUGCCACUUUAGUGGGCGUGCUGCAAAACGUAAAA_AAGAAAAUACUAUUAAUA_CAAAAAAUAAGAA__AAA
...(((((..((((.........))))(....)....)))))((((((((((((....)).))))))))))................................................. (-25.66 = -25.54 +  -0.12)

alignment

secondary structure

dotplot

Window 0

Location	13,182,879 – 13,182,997
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.77
Mean single sequence MFE	-25.88
Consensus MFE	-23.20
Energy contribution	-22.80
Covariance contribution	-0.40
Combinations/Pair	1.20
Mean z-score	-3.07
Structure conservation index	0.90
SVM decision value	4.58
SVM RNA-class probability	0.999924
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13182879 118 + 23771897
AGGCGGCAUGCCACUUUAGUGGGCGUGCUGCAAAACGUAAAAGAAGAAAAUACUAUUAAUAAGAAAAAAUAAGAA--AAAAGUGUAAAAUUUGUGUUAAAAUUAAUGCACGACCGGUAGA
..((((((((((((....)).))))))))))............................................--....(((((.(((((......)))))..))))).......... ( -25.80)
>DroSec_CAF1 34443 117 + 1
AGGCGGCGUGCCACUUUAGUGGGCGUGCUGCAAAACGUAAAAGAAGAAAAUACUAUUAAUA-CAAAAAAUAAGAA--AAAAGUAUAAAAUUUGUGUUAAAAUUAAUGCACGACCGGUAGA
...((((((((..((((.....((((........))))....)))).........((((((-((((.........--............)))))))))).......))))).)))..... ( -23.90)
>DroSim_CAF1 32679 117 + 1
AGGCGGCAUGCCACUUUAGUGGGCGUGCUGCAAAACGUAAAAUAAGAAAAUACUAUUAAUA-CAAAAAAUAAGAA--AAGAGUGUAAAAUUUGUGUUAAAAUUAAUGCACGACCGGUAGA
..((((((((((((....)).)))))))))).....................(((((.(((-(............--....)))).....((((((..........))))))..))))). ( -26.59)
>DroEre_CAF1 37960 115 + 1
AGGCGGCAUGCCACUUUAGUGGGCGUGCUGCAA-AGGUAAAA---GAAAAUACUAUUAAUA-CAAAAAAUAAGAAACAAAAGUGCAAAAUUUGUUCUAAAAUUAAUGCACGACUGGUAGA
..((((((((((((....)).))))))))))..-.((((...---.....)))).......-..............((...(((((.(((((......)))))..)))))...))..... ( -29.00)
>DroYak_CAF1 33661 114 + 1
AGGCGGCAUGCCACUUUAGUGGGCGUGCCACAAAACGUAAAA---GAAAAUACUAUUAAUG-CAAAAAAUGAGAA--AAAAGUGAAAAAUUUGUGUUAAAAUUAAUGCACGACUAGUAGA
..(.((((((((((....)).)))))))).)...........---.....(((((.(..((-((...(((...((--..((((.....))))...))...)))..))))..).))))).. ( -24.10)
>consensus
AGGCGGCAUGCCACUUUAGUGGGCGUGCUGCAAAACGUAAAA_AAGAAAAUACUAUUAAUA_CAAAAAAUAAGAA__AAAAGUGUAAAAUUUGUGUUAAAAUUAAUGCACGACCGGUAGA
..((((((((((((....)).)))))))))).....................(((((......................((((.....))))((((..........))))....))))). (-23.20 = -22.80 +  -0.40)

alignment

secondary structure

dotplot

Window 1

Location	13,182,919 – 13,183,027
Length	108
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.57
Mean single sequence MFE	-17.70
Consensus MFE	-11.84
Energy contribution	-12.42
Covariance contribution	0.58
Combinations/Pair	1.17
Mean z-score	-1.77
Structure conservation index	0.67
SVM decision value	0.21
SVM RNA-class probability	0.633161
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13182919 108 + 23771897
AAGAAGAAAAUACUAUUAAUAAGAAAAAAUAAGAA--AAAAGUGUAAAAUUUGUGUUAAAAUUAAUGCACGACCGGUAGAGAAGGCUGCGCCUUCC----------CUACGCUAAGUAAA
..........((((.....................--....(((((.(((((......)))))..))))).....((((.((((((...)))))).----------))))....)))).. ( -21.10)
>DroSec_CAF1 34483 107 + 1
AAGAAGAAAAUACUAUUAAUA-CAAAAAAUAAGAA--AAAAGUAUAAAAUUUGUGUUAAAAUUAAUGCACGACCGGUAGAGAAGGCUGCGCCUUCC----------CUACGCUAAGUAAA
..........((((.((((((-((((.........--............)))))))))).......((.(....)((((.((((((...)))))).----------))))))..)))).. ( -20.90)
>DroSim_CAF1 32719 107 + 1
AAUAAGAAAAUACUAUUAAUA-CAAAAAAUAAGAA--AAGAGUGUAAAAUUUGUGUUAAAAUUAAUGCACGACCGGUAGAGGAGGCUGCGCCUUCC----------CUACGCUAAGUAAA
..........((((.......-.............--....(((((.(((((......)))))..))))).....((((.((((((...)))))).----------))))....)))).. ( -20.60)
>DroEre_CAF1 37999 90 + 1
AA---GAAAAUACUAUUAAUA-CAAAAAAUAAGAAACAAAAGUGCAAAAUUUGUUCUAAAAUUAAUGCACGACUGGUAGA--------------------------CUGCGCUAAGUAAA
..---.....((((.......-...................(((((.(((((......)))))..)))))...((((...--------------------------....)))))))).. ( -10.10)
>DroYak_CAF1 33701 114 + 1
AA---GAAAAUACUAUUAAUG-CAAAAAAUGAGAA--AAAAGUGAAAAAUUUGUGUUAAAAUUAAUGCACGACUAGUAGAGAAGGCUGUGCCUUCCCUUCCCCUCCCCACGCUAAGUAAA
..---.....((((.......-((.....))....--...((((......((((((..........))))))...(.((.((((((...)))))).)).).........)))).)))).. ( -15.80)
>consensus
AA_AAGAAAAUACUAUUAAUA_CAAAAAAUAAGAA__AAAAGUGUAAAAUUUGUGUUAAAAUUAAUGCACGACCGGUAGAGAAGGCUGCGCCUUCC__________CUACGCUAAGUAAA
........................................((((((....((((((..........))))))........((((((...))))))............))))))....... (-11.84 = -12.42 +   0.58)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:19 2006