Locus 7342

Sequence ID	3L_DroMel_CAF1
Location	19,703,455 – 19,703,597
Length	142
Max. P	0.999614

overview

Window 2

Location	19,703,455 – 19,703,557
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.54
Mean single sequence MFE	-23.55
Consensus MFE	-8.14
Energy contribution	-8.34
Covariance contribution	0.20
Combinations/Pair	1.09
Mean z-score	-3.11
Structure conservation index	0.35
SVM decision value	3.79
SVM RNA-class probability	0.999614
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19703455 102 + 23771897
AUAACAUUUGUUGUUGUACGCCUUGCCAUAUAUACAUACAUACA--UAUAUGUGCGUGAUUGUUGUUCUUUUUAAGCAAACAAAA-AAAA-----------AGAG--CAACAA--AACAG
((((((.....)))))).......(((((((((..........)--)))))).))((..((((((((((((((............-))))-----------))))--))))))--.)).. ( -24.60)
>DroSec_CAF1 17530 117 + 1
AUAACAUUUGUUGUUGUACGCCUUGCCAUAUAUACAUACAUAUGUACAUAUAUGCGUAAUUGUUGUUCUUUUUCAGCAAACCAAA-AAAAAAAAAACAACAAGAG--CAACAAAAAACAG
......(((((((((.......(((((((((((((((....)))))..)))))).))))((((((((.(((((............-..))))).)))))))).))--)))))))...... ( -24.74)
>DroSim_CAF1 19698 106 + 1
AUAACAUUUGUUGUUGUACGCCUUGCCAUAUAUACAUACAUAUGUACAUAUGUGCGUGAUUGUUGUUCUUUUUAAGCAAACCAAA-AAAA-----------AGAG--UAACAAAAAACAG
((((((.....)))))).......(((((((.(((((....))))).))))).))((..((((((((((((((............-))))-----------))))--))))))...)).. ( -23.30)
>DroEre_CAF1 18480 88 + 1
AUAACAUUUGUUGUUGUACGCC-UGCCAUAUAUACG--CGUACA--UACAUAUGCGUGAUUGUUGCUCUU-UUAAGCAAACAG------------------------CUACG--AAACAG
....(((.(((...(((((((.-............)--))))))--.))).)))((((.((((((((...-...))).)))))------------------------.))))--...... ( -21.52)
>DroYak_CAF1 18050 102 + 1
AUAACAUUUGUUGUUGUACGCCUUGCCAUAUAU--------------ACAUAUGCGUGAUUGUUGUUCUUUUUAAGCAAACAGCAACAAA--ACAGCAACAAAACAGCCACC--AAACAG
......(((((((((((.....(..((((((..--------------..))))).)..)((((((((.(((......))).)))))))).--))))))))))).........--...... ( -23.60)
>consensus
AUAACAUUUGUUGUUGUACGCCUUGCCAUAUAUACAUACAUACA__CAUAUAUGCGUGAUUGUUGUUCUUUUUAAGCAAACAAAA_AAAA___________AGAG__CAACAA_AAACAG
((((((.....)))))).....(((((((((((..............))))))).))))(((((..........)))))......................................... ( -8.14 =  -8.34 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	19,703,455 – 19,703,557
Length	102
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.54
Mean single sequence MFE	-25.10
Consensus MFE	-8.23
Energy contribution	-9.14
Covariance contribution	0.91
Combinations/Pair	1.26
Mean z-score	-2.40
Structure conservation index	0.33
SVM decision value	2.18
SVM RNA-class probability	0.989840
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19703455 102 - 23771897
CUGUU--UUGUUG--CUCU-----------UUUU-UUUUGUUUGCUUAAAAAGAACAACAAUCACGCACAUAUA--UGUAUGUAUGUAUAUAUGGCAAGGCGUACAACAACAAAUGUUAU
.((((--((((((--.(((-----------((((-....(....)..))))))).))))))..((((...((((--(((((....))))))))).....))))..))))........... ( -22.10)
>DroSec_CAF1 17530 117 - 1
CUGUUUUUUGUUG--CUCUUGUUGUUUUUUUUUU-UUUGGUUUGCUGAAAAAGAACAACAAUUACGCAUAUAUGUACAUAUGUAUGUAUAUAUGGCAAGGCGUACAACAACAAAUGUUAU
..((((.((((((--...(((((((((((((((.-...........))))))))))))))).(((((.(((((((((((....))))))))))).....))))))))))).))))..... ( -34.30)
>DroSim_CAF1 19698 106 - 1
CUGUUUUUUGUUA--CUCU-----------UUUU-UUUGGUUUGCUUAAAAAGAACAACAAUCACGCACAUAUGUACAUAUGUAUGUAUAUAUGGCAAGGCGUACAACAACAAAUGUUAU
.((((..(((((.--.(((-----------((((-...((....)).)))))))..)))))..((((.(((((((((((....))))))))))).....))))..))))........... ( -25.10)
>DroEre_CAF1 18480 88 - 1
CUGUUU--CGUAG------------------------CUGUUUGCUUAA-AAGAGCAACAAUCACGCAUAUGUA--UGUACG--CGUAUAUAUGGCA-GGCGUACAACAACAAAUGUUAU
.((((.--(((..------------------------((((((((((..-..))))))........((((((((--((....--)))))))))))))-))))...))))........... ( -21.70)
>DroYak_CAF1 18050 102 - 1
CUGUUU--GGUGGCUGUUUUGUUGCUGU--UUUGUUGCUGUUUGCUUAAAAAGAACAACAAUCACGCAUAUGU--------------AUAUAUGGCAAGGCGUACAACAACAAAUGUUAU
......--.(((((...(((((((.(((--.((((((.(.(((......))).).))))))..((((...(((--------------.......)))..))))))).))))))).))))) ( -22.30)
>consensus
CUGUUU_UUGUUG__CUCU___________UUUU_UUUUGUUUGCUUAAAAAGAACAACAAUCACGCAUAUAUA__CAUAUGUAUGUAUAUAUGGCAAGGCGUACAACAACAAAUGUUAU
..((((.((((((..........................((((.........)))).......((((.((((((..(((....)))..)))))).....)))).)))))).))))..... ( -8.23 =  -9.14 +   0.91)

alignment

secondary structure

dotplot

Window 4

Location	19,703,495 – 19,703,597
Length	102
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.76
Mean single sequence MFE	-23.91
Consensus MFE	-14.92
Energy contribution	-14.60
Covariance contribution	-0.32
Combinations/Pair	1.10
Mean z-score	-2.38
Structure conservation index	0.62
SVM decision value	1.94
SVM RNA-class probability	0.983164
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19703495 102 + 23771897
UACA--UAUAUGUGCGUGAUUGUUGUUCUUUUUAAGCAAACAAAA-AAAA-----------AGAG--CAACAA--AACAGCAGCGAUUAAUGGCUGAGCGAUAUGCAAACAGCAAAUGGC
..((--(.....(((((..((((((((((((((............-))))-----------))))--))))))--.))..((((........)))).)))...(((.....))).))).. ( -25.30)
>DroSec_CAF1 17570 117 + 1
UAUGUACAUAUAUGCGUAAUUGUUGUUCUUUUUCAGCAAACCAAA-AAAAAAAAAACAACAAGAG--CAACAAAAAACAGCAGCGAUUAAUGGCUGAGCGAUAUGCAAACAGCAAAUGGC
((((((......)))))).(((((((((((...............-..............)))))--)))))).......((((........)))).((.((.(((.....))).)).)) ( -22.65)
>DroSim_CAF1 19738 106 + 1
UAUGUACAUAUGUGCGUGAUUGUUGUUCUUUUUAAGCAAACCAAA-AAAA-----------AGAG--UAACAAAAAACAGCAGCGAUUAAUGGCUGAGCGAUAUGCAAACAGCAAAUGGC
(((((((....))))))).((((((((((((((............-))))-----------))))--)))))).......((((........)))).((.((.(((.....))).)).)) ( -25.20)
>DroEre_CAF1 18517 91 + 1
UACA--UACAUAUGCGUGAUUGUUGCUCUU-UUAAGCAAACAG------------------------CUACG--AAACAGCAGCGAUUAAUGGCAGAGCGAUAUGCAAACAGCAAAUGGC
....--..(((.(((.(((((((((((.((-((.(((.....)------------------------))..)--))).)))))))))))...(((........))).....))).))).. ( -25.20)
>DroYak_CAF1 18083 109 + 1
-------ACAUAUGCGUGAUUGUUGUUCUUUUUAAGCAAACAGCAACAAA--ACAGCAACAAAACAGCCACC--AAACAGCAGCGAUUAAUGGCAGAGCGAUAUGCAAACAGCAAAUGGC
-------.(((.(((((..((((((((.((((...((.....))...)))--).)))))))).)).((((..--((.(......).))..))))...((.....)).....))).))).. ( -21.20)
>consensus
UACA__CAUAUAUGCGUGAUUGUUGUUCUUUUUAAGCAAACAAAA_AAAA___________AGAG__CAACAA_AAACAGCAGCGAUUAAUGGCUGAGCGAUAUGCAAACAGCAAAUGGC
.............((.(((((((((((...................................................)))))))))))...))...((.((.(((.....))).)).)) (-14.92 = -14.60 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:44:27 2006