Locus 716

Sequence ID	X_DroMel_CAF1
Location	1,973,995 – 1,974,151
Length	156
Max. P	0.937904

overview

Window 9

Location	1,973,995 – 1,974,111
Length	116
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	86.63
Mean single sequence MFE	-42.77
Consensus MFE	-35.90
Energy contribution	-36.30
Covariance contribution	0.40
Combinations/Pair	1.14
Mean z-score	-1.82
Structure conservation index	0.84
SVM decision value	0.27
SVM RNA-class probability	0.663471
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1973995 116 + 22224390
ACGU-GGUGGUUGUGGUUGUGCUGGUGCAACUUGUGGUAAAGGUGCCAGAACUGGUAGUGGUUGUGCUAGCGGUUGAGACAGCCGU---GCUGGCUGUCGUUCUGGCUACUCCAAUCCCA
...(-((.(((((..((.(((((((..(((((.........(.(((((....))))).))))))..)))))......(((((((..---...)))))))......)).))..)))))))) ( -46.20)
>DroSec_CAF1 6878 120 + 1
ACGUAGGUGGUUGUUGUUGUGCUGGUGCAACUUGUGGUAAAGGUGCCAGAACUGGUAGUGGUUGUGCUAGCGGUUGAGACAGCCGUGGUGCUGGCUGUCGUUCUGGCUACUCCAAUCCCG
.....((.(((((..((.(((((((..(((((.........(.(((((....))))).))))))..)))))......((((((((......))))))))......)).))..))))))). ( -45.40)
>DroYak_CAF1 7110 113 + 1
ACGU-GGUGGUUGUGGUUGUGCUGGUACAACUUGUAGUAAAGGUGCCAGAACUGAU---GGUUGUG---GUGGUUGAGCCAGUAGUGGUCGUAGCUGUCGUUUUGGCUACUCCAAUUCCA
....-..(((...(((...(((((((.(((((............((((.(((....---.))).))---))))))).)))))))(((((((.(((....))).))))))).)))...))) ( -36.70)
>consensus
ACGU_GGUGGUUGUGGUUGUGCUGGUGCAACUUGUGGUAAAGGUGCCAGAACUGGUAGUGGUUGUGCUAGCGGUUGAGACAGCCGUGGUGCUGGCUGUCGUUCUGGCUACUCCAAUCCCA
.....((.(((((..((((((....))))))..........(((((((((((.(.((((......)))).)......((((((((......)))))))))))))))).))).))))))). (-35.90 = -36.30 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	1,973,995 – 1,974,111
Length	116
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	86.63
Mean single sequence MFE	-30.86
Consensus MFE	-25.23
Energy contribution	-26.90
Covariance contribution	1.67
Combinations/Pair	1.00
Mean z-score	-2.79
Structure conservation index	0.82
SVM decision value	1.26
SVM RNA-class probability	0.937904
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1973995 116 - 22224390
UGGGAUUGGAGUAGCCAGAACGACAGCCAGC---ACGGCUGUCUCAACCGCUAGCACAACCACUACCAGUUCUGGCACCUUUACCACAAGUUGCACCAGCACAACCACAACCACC-ACGU
(((...(((....(((((((((((((((...---..)))))))......(.(((........))).).)))))))).............((.((....))))..)))...)))..-.... ( -36.20)
>DroSec_CAF1 6878 120 - 1
CGGGAUUGGAGUAGCCAGAACGACAGCCAGCACCACGGCUGUCUCAACCGCUAGCACAACCACUACCAGUUCUGGCACCUUUACCACAAGUUGCACCAGCACAACAACAACCACCUACGU
.(((..(((((..(((((((((((((((........)))))))......(.(((........))).).))))))))..)))))......((((........))))........))).... ( -36.30)
>DroYak_CAF1 7110 113 - 1
UGGAAUUGGAGUAGCCAAAACGACAGCUACGACCACUACUGGCUCAACCAC---CACAACC---AUCAGUUCUGGCACCUUUACUACAAGUUGUACCAGCACAACCACAACCACC-ACGU
(((...(((.(((((..........)))))........((((..((((..(---((.(((.---....))).)))..............))))..)))).....)))...)))..-.... ( -20.09)
>consensus
UGGGAUUGGAGUAGCCAGAACGACAGCCAGCACCACGGCUGUCUCAACCGCUAGCACAACCACUACCAGUUCUGGCACCUUUACCACAAGUUGCACCAGCACAACCACAACCACC_ACGU
.((...(((((..(((((((((((((((........)))))))......(....).............))))))))..)))))......((((........)))).....))........ (-25.23 = -26.90 +   1.67)

alignment

secondary structure

dotplot

Window 1

Location	1,974,034 – 1,974,151
Length	117
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	87.22
Mean single sequence MFE	-30.73
Consensus MFE	-23.33
Energy contribution	-25.33
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-2.49
Structure conservation index	0.76
SVM decision value	0.62
SVM RNA-class probability	0.802697
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1974034 117 - 22224390
CGUCCGCAACAUCAACAUCAACCACGACAACGAUCACCAAUGGGAUUGGAGUAGCCAGAACGACAGCCAGC---ACGGCUGUCUCAACCGCUAGCACAACCACUACCAGUUCUGGCACCU
..........................((..(((((.((...)))))))..)).(((((((((((((((...---..)))))))......(.(((........))).).)))))))).... ( -34.70)
>DroSec_CAF1 6918 120 - 1
CGUCCGCAACAUCAACUUCAACCACGACGACGAUCACCAACGGGAUUGGAGUAGCCAGAACGACAGCCAGCACCACGGCUGUCUCAACCGCUAGCACAACCACUACCAGUUCUGGCACCU
..............(((((((((.((..(........)..)))).))))))).(((((((((((((((........)))))))......(.(((........))).).)))))))).... ( -37.80)
>DroYak_CAF1 7149 114 - 1
CGUCCGCAACAUCAACUUCUACCACGACGACGAUCACCAAUGGAAUUGGAGUAGCCAAAACGACAGCUACGACCACUACUGGCUCAACCAC---CACAACC---AUCAGUUCUGGCACCU
.(((((.((((((..(.((......)).)..))).....((((...(((.(((((..........)))))(((((....))).)).....)---))...))---))..))).))).)).. ( -19.70)
>consensus
CGUCCGCAACAUCAACUUCAACCACGACGACGAUCACCAAUGGGAUUGGAGUAGCCAGAACGACAGCCAGCACCACGGCUGUCUCAACCGCUAGCACAACCACUACCAGUUCUGGCACCU
..........................((..(((((.((...)))))))..)).(((((((((((((((........)))))))......(....).............)))))))).... (-23.33 = -25.33 +   2.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:54 2006