Locus 140

Sequence ID	2R_DroMel_CAF1
Location	1,401,819 – 1,402,069
Length	250
Max. P	0.948541

overview

Window 2

Location	1,401,819 – 1,401,923
Length	104
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	81.71
Mean single sequence MFE	-39.25
Consensus MFE	-27.83
Energy contribution	-29.50
Covariance contribution	1.67
Combinations/Pair	1.00
Mean z-score	-1.54
Structure conservation index	0.71
SVM decision value	-0.05
SVM RNA-class probability	0.507996
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1401819 104 + 20766785
CUA-UAGCGGCAGCAGGCCCUGGAGUGGGUGGAAUGGGUGUAGUGGGUGAAACUCCCAAGCUCCUACUCCCUGCUCCUGUUCCUUUCUGACU------CUGCUCCUGCUCC---------
...-....((.((((((...((((((.((.((((((((.((((.(((((...............))))).)))).))))))))...)).)))------)))..))))))))--------- ( -40.76)
>DroSec_CAF1 27683 110 + 1
CAACUAGCGACAGCAGGCCCUGGAGUGGGUG---------UAGUGGGUGG-ACUCCCAGGCUCCUACUCCCUGCUCCUGUUCCUUUCUGAUUCUGAUUCUGCUCCUGCUCCUGCUCCUGC
......(((..((((((....((((..((.(---------(((.((((((-(((....)).))).)))).)))).))..)))).................((....)).))))))..))) ( -36.50)
>DroSim_CAF1 32634 110 + 1
CAACUAGCGACAGCAGGCCCUGGAGUGGGUGUAGUGGGUGUAGUGGGUGG-ACUCCCAGGCUCCUACUCCCUGCUCCUGUUCCUUUCUGAUUCUGAUUCUGCUCCUGCUCC---------
.....((((..((((((....((((..((.(.((((((.((..((((...-...)))).)).)))))))))..))))........((.......)).))))))..))))..--------- ( -40.50)
>consensus
CAACUAGCGACAGCAGGCCCUGGAGUGGGUG_A_UGGGUGUAGUGGGUGG_ACUCCCAGGCUCCUACUCCCUGCUCCUGUUCCUUUCUGAUUCUGAUUCUGCUCCUGCUCC_________
.....((((..(((((.....((((..((.(...((((.((..((((.......)))).)).))))..)))..))))...((......))........)))))..))))........... (-27.83 = -29.50 +   1.67)

alignment

secondary structure

dotplot

Window 3

Location	1,401,923 – 1,402,029
Length	106
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.08
Mean single sequence MFE	-31.17
Consensus MFE	-23.35
Energy contribution	-24.23
Covariance contribution	0.87
Combinations/Pair	1.03
Mean z-score	-1.45
Structure conservation index	0.75
SVM decision value	0.02
SVM RNA-class probability	0.542744
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1401923 106 - 20766785
AC----------ACACA-CAGCGACAUUGUCGGUGGUAUAAACAAUUUAAAACUUGUAAAUAUUUUCGUGGUAAUCCGCUUUGUCGCCACUUGGCAGUCGAUGCGGAUGCAGGAACA---
..----------.(((.-((.((((...)))).))((((..((((........))))..))))....)))(((.(((((.(((.((((....))).).))).)))))))).......--- ( -28.40)
>DroSec_CAF1 27793 111 - 1
ACA--------CACACA-CAGCGACACUGUCGGUGGUAUAAACAAUUUAAAACUUGUAAAUAUUUUCGUGGUAAUCCGCUUUGUCGCCACUUGGCUGUCGAUGCGGAUGCAGGAACAGGG
...--------...((.-((.((((...)))).))))...............(((((........((.((...((((((.(((.((((....))).).))).)))))).)).))))))). ( -29.30)
>DroEre_CAF1 26656 108 - 1
UCACACACAC---------ACCGACACUGGCGGUGGCAUAAACAAUUUAAAACUUGUAAAUAUUUUCGUGGUAAUCCGCUUUGUCGCCACUUGGCUGUGGAUGCGGACGCAGGAGCG---
..((.(((.(---------((((.......)))))......((((........))))..........)))))..(((((((..(.(((....))).)..)).)))))(((....)))--- ( -29.40)
>DroYak_CAF1 28448 117 - 1
ACACAUACACACACACACCACCGACACUGUCGGUGGUAUAAACAAUUUAAAACUUGUAAAUAUUUUCGUGGUAAUCCGCUUUGUUGCCACUUGGCUGUGGAUGCGGAUGCAGGAACA---
.....(((.(((....(((((((((...)))))))))....((((........))))..........))))))((((((((..(.(((....))).)..)).)))))).........--- ( -37.60)
>consensus
ACA_________ACACA_CACCGACACUGUCGGUGGUAUAAACAAUUUAAAACUUGUAAAUAUUUUCGUGGUAAUCCGCUUUGUCGCCACUUGGCUGUCGAUGCGGAUGCAGGAACA___
..................(((((((...)))))))((....((((........))))........((.((...((((((((..(.(((....))).)..)).)))))).)).)))).... (-23.35 = -24.23 +   0.87)

alignment

secondary structure

dotplot

Window 4

Location	1,401,960 – 1,402,069
Length	109
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	86.83
Mean single sequence MFE	-30.33
Consensus MFE	-23.33
Energy contribution	-24.20
Covariance contribution	0.87
Combinations/Pair	1.10
Mean z-score	-2.00
Structure conservation index	0.77
SVM decision value	0.83
SVM RNA-class probability	0.860734
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1401960 109 + 20766785
AGCGGAUUACCACGAAAAUAUUUACAAGUUUUAAAUUGUUUAUACCACCGACAAUGUCGCUG-UGUGU----------GUGUGUUAUCUGGCAUAUUAUUAUUUAUGCCAUUGGGCAUCA
.((((((.(((((..........((((........))))..((((((.((((...)))).))-.))))----------))).)).))))((((((........)))))).....)).... ( -25.50)
>DroSec_CAF1 27833 111 + 1
AGCGGAUUACCACGAAAAUAUUUACAAGUUUUAAAUUGUUUAUACCACCGACAGUGUCGCUG-UGUGUG--------UGUGUGUUAUCUGGCAUAUUAUUAUUUAUGCCAUUAGGCAUCA
.((((((.((((((....(((..((((........))))..))).(((..((((.....)))-)..)))--------)))).)).))))((((((........)))))).....)).... ( -26.90)
>DroEre_CAF1 26693 111 + 1
AGCGGAUUACCACGAAAAUAUUUACAAGUUUUAAAUUGUUUAUGCCACCGCCAGUGUCGGU---------GUGUGUGUGAGUGUUAUCCGGCGUAUUAUUAUUUAUGCCAUUGGGCAUCG
.(((((((((((((....(((..((((........))))..))).(((((((......)))---------).))))))).)))..))))((((((........)))))).....)).... ( -30.00)
>DroYak_CAF1 28485 120 + 1
AGCGGAUUACCACGAAAAUAUUUACAAGUUUUAAAUUGUUUAUACCACCGACAGUGUCGGUGGUGUGUGUGUGUAUGUGUGUGUUAUCCGGCAUAUUAUUAUUUAUGCAAUUGGGCAUCG
.((((((.((((((...((((.((((..............((((((((((((...)))))))))))))))).)))).)))).)).)))).(((((........)))))......)).... ( -38.93)
>consensus
AGCGGAUUACCACGAAAAUAUUUACAAGUUUUAAAUUGUUUAUACCACCGACAGUGUCGCUG_UGUGU_________UGUGUGUUAUCCGGCAUAUUAUUAUUUAUGCCAUUGGGCAUCA
.((((((.(((((.....(((..((((........))))..))).(((((((...)))))))................))).)).))))((((((........)))))).....)).... (-23.33 = -24.20 +   0.87)

alignment

secondary structure

dotplot

Window 5

Location	1,401,960 – 1,402,069
Length	109
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.83
Mean single sequence MFE	-24.80
Consensus MFE	-19.09
Energy contribution	-19.90
Covariance contribution	0.81
Combinations/Pair	1.08
Mean z-score	-2.43
Structure conservation index	0.77
SVM decision value	1.38
SVM RNA-class probability	0.948541
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1401960 109 - 20766785
UGAUGCCCAAUGGCAUAAAUAAUAAUAUGCCAGAUAACACAC----------ACACA-CAGCGACAUUGUCGGUGGUAUAAACAAUUUAAAACUUGUAAAUAUUUUCGUGGUAAUCCGCU
....((....(((((((........)))))))(((.((.(((----------.....-((.((((...)))).))((((..((((........))))..))))....))))).))).)). ( -23.00)
>DroSec_CAF1 27833 111 - 1
UGAUGCCUAAUGGCAUAAAUAAUAAUAUGCCAGAUAACACACA--------CACACA-CAGCGACACUGUCGGUGGUAUAAACAAUUUAAAACUUGUAAAUAUUUUCGUGGUAAUCCGCU
....((....(((((((........)))))))(((.((.(((.--------......-((.((((...)))).))((((..((((........))))..))))....))))).))).)). ( -23.00)
>DroEre_CAF1 26693 111 - 1
CGAUGCCCAAUGGCAUAAAUAAUAAUACGCCGGAUAACACUCACACACAC---------ACCGACACUGGCGGUGGCAUAAACAAUUUAAAACUUGUAAAUAUUUUCGUGGUAAUCCGCU
..(((((....)))))............((.((((..(((.........(---------((((.......)))))......((((........))))..........)))...)))))). ( -22.90)
>DroYak_CAF1 28485 120 - 1
CGAUGCCCAAUUGCAUAAAUAAUAAUAUGCCGGAUAACACACACAUACACACACACACCACCGACACUGUCGGUGGUAUAAACAAUUUAAAACUUGUAAAUAUUUUCGUGGUAAUCCGCU
............(((((........)))))(((((.((.(((..............(((((((((...)))))))))....((((........))))..........))))).))))).. ( -30.30)
>consensus
CGAUGCCCAAUGGCAUAAAUAAUAAUAUGCCAGAUAACACACA_________ACACA_CACCGACACUGUCGGUGGUAUAAACAAUUUAAAACUUGUAAAUAUUUUCGUGGUAAUCCGCU
..(((((...(((((((........)))))))...........................((((((...)))))))))))..((((........))))..........((((....)))). (-19.09 = -19.90 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:29:17 2006