Locus 3124

Sequence ID	2R_DroMel_CAF1
Location	10,671,283 – 10,671,405
Length	122
Max. P	0.760370

overview

Window 4

Location	10,671,283 – 10,671,387
Length	104
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	69.14
Mean single sequence MFE	-15.67
Consensus MFE	-5.51
Energy contribution	-5.59
Covariance contribution	0.09
Combinations/Pair	1.17
Mean z-score	-1.95
Structure conservation index	0.35
SVM decision value	0.50
SVM RNA-class probability	0.760370
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10671283 104 - 20766785
ACAGUAAAUAAUACUCGAACCCCUGGACACAGGAUUUUCAUUCAUCCGCACACACACAGGACACCGAAAA-AAAGUCCU---------AUAAACUAAAAAAAAUUUAGUGUCUA-----
..((((.....))))........(((((((.((((........))))..........(((((........-...)))))---------...................)))))))----- ( -17.70)
>DroSec_CAF1 8165 105 - 1
ACAGUAAAUAAUACUCGAACCCCUGGACACAGGAUUUCCAUUCAUCCCCACACAUACAGGACACCGAAAAAAAAAUCCU---------AUAAACUAAAAAAAAACUAGUUUCUA-----
..((((.....)))).(((..((((....))))..)))...................((((..............))))---------..((((((.........))))))...----- ( -10.24)
>DroSim_CAF1 8267 103 - 1
ACAGUAAAUAAUACUCGAACCCCUGGACACAGGAUUUCCAUUCAUCCGCACACACACGGGACACCGAAA--AAAAUCCU---------AUAAACUAAAAUAAAAUUAGUUUCUA-----
..((((.....)))).(((..((((....))))..)))..................(((....)))...--........---------..(((((((.......)))))))...----- ( -14.00)
>DroEre_CAF1 8243 119 - 1
ACAGUAAAUAAUACUGGAAGCGCUGGACACAGGAUUUCCAUUCAUCCGCACACACACAGCACACUGAAAAAAAUGCCUUUCAGUUGCUUCUAGUUGUAAAAACAUUUUUUACCAAAUUC
............(((((((((((((......((((........)))).........))))..(((((((........))))))).))))))))).((((((.....))))))....... ( -28.86)
>DroYak_CAF1 8479 94 - 1
ACAGUAAACAAUACU---------GGACACAGGAUUUCCAUUCAUCCACACACACACA---------AAAAAAUACCCUUGCAUU--UUCAGACUGAAUAAAUAUUACUGUCUA-----
.(((((.....))))---------)((((..((((........))))...........---------..................--(((.....)))..........))))..----- ( -10.60)
>DroAna_CAF1 8120 97 - 1
ACAGUAAACAAUACUUAGGCUCCUGGCCACCGGAUUUCCUUUCAUCCAUACCCACAAAGGACACUCAGAAAAACA--UG---------AUAAAGUUUAGGAAUAUUU------A-----
.............(((((((((((((...))((((........))))..........))))...(((........--))---------)....))))))).......------.----- ( -12.60)
>consensus
ACAGUAAAUAAUACUCGAACCCCUGGACACAGGAUUUCCAUUCAUCCGCACACACACAGGACACCGAAAAAAAAAUCCU_________AUAAACUAAAAAAAAAUUAGUUUCUA_____
..((((.....))))......((((......((((........)))).........))))........................................................... ( -5.51 =  -5.59 +   0.09)

alignment

secondary structure

dotplot

Window 5

Location	10,671,309 – 10,671,405
Length	96
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	79.85
Mean single sequence MFE	-27.07
Consensus MFE	-18.00
Energy contribution	-19.67
Covariance contribution	1.67
Combinations/Pair	1.19
Mean z-score	-1.26
Structure conservation index	0.66
SVM decision value	0.01
SVM RNA-class probability	0.536782
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10671309 96 + 20766785
AGGACUUU-UUUUCGGUGUCCUGUGUGUGUGCGGAUGAAUGAAAAUCCUGUGUCCAGGGGUUCGAGUAUUAUUUACUGUAUCAACACGCUGGGAGCA
........-......((..((.((((((((((((.(((((((((..((((....))))..))......)))))))))))))..)))))).))..)). ( -25.50)
>DroSec_CAF1 8191 97 + 1
AGGAUUUUUUUUUCGGUGUCCUGUAUGUGUGGGGAUGAAUGGAAAUCCUGUGUCCAGGGGUUCGAGUAUUAUUUACUGUAUCAACACGCUGGGCGCA
(((((((((..((((...(((..(....)..))).)))).)))))))))((((((((.((((..((((.....)))).....))).).)))))))). ( -33.00)
>DroSim_CAF1 8293 95 + 1
AGGAUUUU--UUUCGGUGUCCCGUGUGUGUGCGGAUGAAUGGAAAUCCUGUGUCCAGGGGUUCGAGUAUUAUUUACUGUAUCAACAUGCUGGGCGCA
.(((....--.))).((((((.((((((((((((.(((((((((..((((....))))..)))......))))))))))))..)))))).)))))). ( -30.30)
>DroEre_CAF1 8283 97 + 1
AAGGCAUUUUUUUCAGUGUGCUGUGUGUGUGCGGAUGAAUGGAAAUCCUGUGUCCAGCGCUUCCAGUAUUAUUUACUGUAUCAACACGCUGGGCGUA
.(((.((((((((((.((..(.......)..))..)))).)))))))))..((((((((....(((((.....)))))........))))))))... ( -29.00)
>DroYak_CAF1 8512 79 + 1
AGGGUAUUUUUU---------UGUGUGUGUGUGGAUGAAUGGAAAUCCUGUGUCC---------AGUAUUGUUUACUGUAUCAACACGCUGGGCGUA
(((((.((..((---------..(.(......).)..))..)).)))))..((((---------(((..((((.........)))).)))))))... ( -17.40)
>DroAna_CAF1 8140 95 + 1
CA--UGUUUUUCUGAGUGUCCUUUGUGGGUAUGGAUGAAAGGAAAUCCGGUGGCCAGGAGCCUAAGUAUUGUUUACUGUAUCAACACACUGGGCGCC
..--...........((((((..(((((((.(((((........)))))...)))..((.....((((.....))))...))..))))..)))))). ( -27.20)
>consensus
AGGAUUUUUUUUUCGGUGUCCUGUGUGUGUGCGGAUGAAUGGAAAUCCUGUGUCCAGGGGUUCGAGUAUUAUUUACUGUAUCAACACGCUGGGCGCA
...............((((((.(((((((((((((((...((....))..))))).........((((.....))))))))..)))))).)))))). (-18.00 = -19.67 +   1.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:07 2006