Locus 7026

Sequence ID	3L_DroMel_CAF1
Location	19,007,979 – 19,008,186
Length	207
Max. P	0.999039

overview

Window 3

Location	19,007,979 – 19,008,083
Length	104
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	83.08
Mean single sequence MFE	-31.00
Consensus MFE	-24.06
Energy contribution	-22.94
Covariance contribution	-1.12
Combinations/Pair	1.23
Mean z-score	-1.50
Structure conservation index	0.78
SVM decision value	-0.01
SVM RNA-class probability	0.528586
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19007979 104 - 23771897
UCGAUGCCGCGAUGGAGGUGGAGUUGGCCCGUUGCUUAUGGAUGCACUGGGAAAAAAUUCCAUUGUUUUGUGACACUUUAAUCCUAA-GACAUUACAUUAAUAAU-------
..((((.(((((....(((((((((..((((.(((........))).))))....)))))))))...)))))...(((.......))-).))))...........------- ( -25.80)
>DroSec_CAF1 141492 110 - 1
UCGAUGCCGCAAUGGAGGUGGAGUUGGCCCGUUGCUGAUGGAUGCACUGGGAA-AAAUUCCAUUGUUUUGUGACACUUUUAUCCUAA-GACAUUACAUUAAUAAUAGAUCAU
..(((..(((((....(((((((((..((((.(((........))).))))..-.)))))))))...)))))...(((.......))-)..................))).. ( -27.00)
>DroSim_CAF1 147391 111 - 1
UCGAUGCCGCAAUGGAGGUGGAGUUGGCCCGUUGCUGAUGGAUGCACUGGGAAAAAAUUCCAUUGUUAUGUGACAGUUUAAUCCUAA-GACAUUACAUUAAUAAUGGAUCAU
(((((.((((.......)))).)))))((((.(((........))).)))).......(((((((((((((((..((((.......)-))).))))).)))))))))).... ( -31.10)
>DroEre_CAF1 143057 111 - 1
UCGAUGCCGCAAUGGAGGUGGAGUUGCCCCGUUGCUGAUGGAUGUACUGGGAA-AAAUUUCGCUGUCCUAGGACACUCAAAUCCCAAAAAAGUGACAUUAAUAAUGGGUCAA
..(((.(((((((((.(((......))))))))))(((((....((((((((.-...(((.(.((((....)))).).))))))).....)))).))))).....))))).. ( -30.20)
>DroYak_CAF1 163303 104 - 1
UCGAUGCCGCGAUGGAGGUGGAGUUGGCCCGUUGCUGAUGGAUGUACUGGGAA-AAAUUUCACUGUCCUAGGACACUUAAAUCCUAG-AAAGUGGCAU------UGGGUCAU
((((((((((...(..(((((((((..((((.(((........))).))))..-.)))))))))..)((((((........))))))-...)))))))------)))..... ( -40.90)
>consensus
UCGAUGCCGCAAUGGAGGUGGAGUUGGCCCGUUGCUGAUGGAUGCACUGGGAA_AAAUUCCAUUGUUCUGUGACACUUUAAUCCUAA_GACAUUACAUUAAUAAUGGAUCAU
.............((((((((((((..((((.(((........))).))))....)))))))))(((....))).......)))............................ (-24.06 = -22.94 +  -1.12)

alignment

secondary structure

dotplot

Window 4

Location	19,008,050 – 19,008,159
Length	109
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	79.52
Mean single sequence MFE	-31.44
Consensus MFE	-24.22
Energy contribution	-24.00
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-2.40
Structure conservation index	0.77
SVM decision value	1.45
SVM RNA-class probability	0.955103
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19008050 109 + 23771897
AACGGGC---CAACUCCACCUCCAUCGCGGCAUCGA-CUUGCCUUCGGUUUUACCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCG
...(((.---....)))......((((.((((....-..))))..)))).(((((((...)))))))(((((((.((.((((((((....)))))))))))))))))...... ( -32.90)
>DroPse_CAF1 148996 87 + 1
--------------------------AUGGCUUUACCUUUACCUUUGCCUUUGCCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCG
--------------------------..(((...............))).(((((((...)))))))(((((((.((.((((((((....)))))))))))))))))...... ( -26.96)
>DroEre_CAF1 143135 109 + 1
AACGGGG---CAACUCCACCUCCAUUGCGGCAUCGA-CUUGCCUUCGGUUUUACCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCG
...(((.---...).))((((...((((((((....-..))))...((.....)).)))).))))..(((((((.((.((((((((....)))))))))))))))))...... ( -36.00)
>DroYak_CAF1 163374 109 + 1
AACGGGC---CAACUCCACCUCCAUCGCGGCAUCGA-CUUGCCUUCGGUUUUACCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCG
...(((.---....)))......((((.((((....-..))))..)))).(((((((...)))))))(((((((.((.((((((((....)))))))))))))))))...... ( -32.90)
>DroAna_CAF1 139442 112 + 1
AAUGGGCAGCAAACUCCACCUCCGUCGUGGCAUCGA-CUUCGGUUCGAUUUUACCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCG
...............((((.......)))).(((((-(....).))))).(((((((...)))))))(((((((.((.((((((((....)))))))))))))))))...... ( -32.90)
>DroPer_CAF1 150135 87 + 1
--------------------------AUGGCUUUACCUUUACCUUUGCCUUUGCCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCG
--------------------------..(((...............))).(((((((...)))))))(((((((.((.((((((((....)))))))))))))))))...... ( -26.96)
>consensus
AACGGGC___CAACUCCACCUCCAUCGCGGCAUCGA_CUUGCCUUCGGUUUUACCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCG
..................................................(((((((...)))))))(((((((.((.((((((((....)))))))))))))))))...... (-24.22 = -24.00 +  -0.22)

alignment

secondary structure

dotplot

Window 5

Location	19,008,083 – 19,008,186
Length	103
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	90.15
Mean single sequence MFE	-26.97
Consensus MFE	-24.22
Energy contribution	-24.00
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-3.36
Structure conservation index	0.90
SVM decision value	3.34
SVM RNA-class probability	0.999039
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19008083 103 + 23771897
CUUGCCUUCGGUUUUACCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCGCUUGAUUUUCAUUUUUUGUACGACUCU-----
.......(((...(((((((...)))))))(((((((.((.((((((((....)))))))))))))))))..........................)))....----- ( -26.20)
>DroPse_CAF1 149007 96 + 1
UUUACCUUUGCCUUUGCCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCGCUUUAUUUUCAUUUUU-------CUCU-----
.((((((((((........)))).))))))(((((((.((.((((((((....)))))))))))))))))......................-------....----- ( -26.30)
>DroSim_CAF1 147502 103 + 1
CUUGCCUUCGGUUUUACCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCGCUUGAUUUUCAUUUUUUGUACGACUCU-----
.......(((...(((((((...)))))))(((((((.((.((((((((....)))))))))))))))))..........................)))....----- ( -26.20)
>DroEre_CAF1 143168 101 + 1
CUUGCCUUCGGUUUUACCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCGCUUGAUUUUCAUUUUUUGUCCGACU-------
.......((((..(((((((...)))))))(((((((.((.((((((((....))))))))))))))))).........................))))..------- ( -28.40)
>DroYak_CAF1 163407 103 + 1
CUUGCCUUCGGUUUUACCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCGCUUGAUUUUCAUUUUUUAUCCGACUCU-----
.......((((..(((((((...)))))))(((((((.((.((((((((....))))))))))))))))).........................))))....----- ( -28.40)
>DroPer_CAF1 150146 101 + 1
UUUACCUUUGCCUUUGCCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCGCUUUAUUUUCAUUUUU-------CUCUCUCUC
.((((((((((........)))).))))))(((((((.((.((((((((....)))))))))))))))))......................-------......... ( -26.30)
>consensus
CUUGCCUUCGGUUUUACCUGCAACAGGUAAGAAAUGUUCGUACGUUGUUUUUAAACGGCGUCGGCAUUUCAAUUCGCUUGAUUUUCAUUUUUUGU_CGACUCU_____
.............(((((((...)))))))(((((((.((.((((((((....)))))))))))))))))...................................... (-24.22 = -24.00 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:50 2006