Locus 1076

Sequence ID	2L_DroMel_CAF1
Location	2,975,860 – 2,976,084
Length	224
Max. P	0.787265

overview

Window 1

Location	2,975,860 – 2,975,973
Length	113
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	92.92
Mean single sequence MFE	-30.09
Consensus MFE	-24.64
Energy contribution	-25.36
Covariance contribution	0.72
Combinations/Pair	1.07
Mean z-score	-1.57
Structure conservation index	0.82
SVM decision value	0.58
SVM RNA-class probability	0.787265
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2975860 113 + 22407834
CCAGCCAUUGGCGGGAGUUCUUGUCCAUGCAGACAACUUGGAUCAUUCCAGUAAGAAAUUGAAUGCCCCCAAAAUUGAUGCUGGACUUCCAACCCUUUUUCAACUCCUCCACA
........(((.(((((((.(((((......))))).(((((....(((((((...((((............))))..)))))))..))))).........)))))))))).. ( -28.40)
>DroSec_CAF1 5842 113 + 1
CCAGCCACUCGCGGGAGUUCUUGUCCAUGCAGACAACUUGGAUCAUUCCAGUAAGGAAUUCGAUGCCCCAAAAGUUGAUGCUGGACUUCCAACCCUUUUUCAACUCCUCCACA
..........(.(((((((...(((((.(((..((((((((((((((((.....)))))..))).))....)))))).))))))))...............))))))).)... ( -29.57)
>DroSim_CAF1 5837 113 + 1
CCAGCCACUCGCGGGAGUUCUUGUCCAUGCAGACAACUUGGAUCAUUCCAGUAAGGAAUUCGAUGCCCCAAAAGUUGAUGCUGGACUUCCAACCCUUUUUCAACUCCUCCACA
..........(.(((((((...(((((.(((..((((((((((((((((.....)))))..))).))....)))))).))))))))...............))))))).)... ( -29.57)
>DroEre_CAF1 5979 113 + 1
CCAGCCAUUGGCGGGAGUUCUUGUCCAUGCAGACGAUUUGGAUCAGUCCGGAAAGGAAUUGGAUGCCCCCAAAGUUGAUGCUGGACUUCCAACCCUUUUUCAUUUCCUCCACA
........(((.((((((..(((((......))))).(((((..(((((((...((..((((......))))..))....)))))))))))).........)))))).))).. ( -30.90)
>DroYak_CAF1 5942 113 + 1
CCAGCCAUUGGCGGGAGUUCUUGUCCAUGCAGACAACUUGGAUCAGUCCAGAGAGGAAUUGGAUGCCCCCAAAGUUGAUGCUGGACUUCCAACCCUUUUUCAUUUCCUCCACC
...(((...)))(((.......(((((.(((..((((((((....((((((.......))))))....)).)))))).))))))))......))).................. ( -32.02)
>consensus
CCAGCCAUUGGCGGGAGUUCUUGUCCAUGCAGACAACUUGGAUCAUUCCAGUAAGGAAUUGGAUGCCCCCAAAGUUGAUGCUGGACUUCCAACCCUUUUUCAACUCCUCCACA
...((.....))(((.......(((((.(((..((((((((((((((((.....)))))..))).))....)))))).))))))))......))).................. (-24.64 = -25.36 +   0.72)

alignment

secondary structure

dotplot

Window 2

Location	2,975,973 – 2,976,084
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.76
Mean single sequence MFE	-35.26
Consensus MFE	-20.96
Energy contribution	-20.64
Covariance contribution	-0.32
Combinations/Pair	1.19
Mean z-score	-2.04
Structure conservation index	0.59
SVM decision value	0.40
SVM RNA-class probability	0.723080
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2975973 111 + 22407834
AGGCCGGCUUCGAUCUCAUGCAAUUGCUGAUUAGUCAGCUCGCAAUCCGGAUAAGUUUCCGCCAUUAUUGCCAUGGUAAUACUAUUCUGUUUCGAGG------UCCAU---GACGGCUCU
.(((((.....((((((.(((....(((((....)))))..)))...((((......))))....((((((....))))))............))))------))...---..))))).. ( -34.10)
>DroSec_CAF1 5955 111 + 1
AGGCCGGCUUCGAUCUCUUGCAAUUGCUGAUUGGUCAGCUCGCAAUCCGGAUAAUUUUCCGCCAUUACUGUCAUGGUAAUACUAUUCUGAUUGAAGG------CCCAU---AACGGCUCU
.((((((((((((((..((((....(((((....)))))..))))..((((......))))..((((((.....))))))........))))))).)------))...---...)))).. ( -32.00)
>DroSim_CAF1 5950 111 + 1
AGGCCGGCUUCGAUCUCUUGCAAUUGCUGAUUGGUCAGCUCGCAAUCCGGAUAAUUUUCCGCCAUUACUGCCAUGGUAAUACUAUUCUGAUUGAAGG------UCCAU---AACGGCCCU
.(((((.((((((((..((((....(((((....)))))..))))..((((......))))..((((((.....))))))........)))))))).------.....---..))))).. ( -33.90)
>DroEre_CAF1 6092 120 + 1
AGACCGUCUUCGAUCUCAUGCAGUUGCUUAUUAGUGAGCACGCAAUCGGGAUAAUUUUCCGCCAUUACUGCCAUGGUAAAACCAUUUUGCUUGGAGCCCAGUGCCCUUGAAGACGGGUCC
...((((((((((...((((((((((((((....))))))......(((((.....))))).....)))).))))(((((.....)))))..((.((.....)))))))))))))).... ( -36.70)
>DroYak_CAF1 6055 120 + 1
AAGCCGUCUUCGAUCUCAUGCAGUUGCUUAUUAGUCAGCAAGCAAUCCGGAUAAGUUUCUGCCAUAAUUGCCAUGGUAAGACCAUUCUGCUUCGUGCUUAGUGCCCGUGAAGACGGCUCU
.(((((((((((....(((...((((((....)).))))(((((...((((...((((.((((((.......))))))))))...)))).....))))).)))....))))))))))).. ( -39.60)
>consensus
AGGCCGGCUUCGAUCUCAUGCAAUUGCUGAUUAGUCAGCUCGCAAUCCGGAUAAUUUUCCGCCAUUACUGCCAUGGUAAUACUAUUCUGAUUGGAGG______CCCAU___GACGGCUCU
.(((((............(((....(((((....)))))..)))....(((......)))(((((.......)))))....................................))))).. (-20.96 = -20.64 +  -0.32)

alignment

secondary structure

dotplot

Window 3

Location	2,975,973 – 2,976,084
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	81.76
Mean single sequence MFE	-36.81
Consensus MFE	-16.14
Energy contribution	-17.74
Covariance contribution	1.60
Combinations/Pair	1.00
Mean z-score	-2.29
Structure conservation index	0.44
SVM decision value	0.10
SVM RNA-class probability	0.585554
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2975973 111 - 22407834
AGAGCCGUC---AUGGA------CCUCGAAACAGAAUAGUAUUACCAUGGCAAUAAUGGCGGAAACUUAUCCGGAUUGCGAGCUGACUAAUCAGCAAUUGCAUGAGAUCGAAGCCGGCCU
((.((((((---(((((------(.((......))...))....)))))))......((((((......))).(((((((((((((....)))))..)))))....)))...)))))))) ( -32.00)
>DroSec_CAF1 5955 111 - 1
AGAGCCGUU---AUGGG------CCUUCAAUCAGAAUAGUAUUACCAUGACAGUAAUGGCGGAAAAUUAUCCGGAUUGCGAGCUGACCAAUCAGCAAUUGCAAGAGAUCGAAGCCGGCCU
((.((((((---((((.------.....................)))))))......((((((......)))...(((((((((((....)))))..)))))).........)))))))) ( -32.45)
>DroSim_CAF1 5950 111 - 1
AGGGCCGUU---AUGGA------CCUUCAAUCAGAAUAGUAUUACCAUGGCAGUAAUGGCGGAAAAUUAUCCGGAUUGCGAGCUGACCAAUCAGCAAUUGCAAGAGAUCGAAGCCGGCCU
.((((((((---(((((------(.(((.....)))..))....)))))))......((((((......)))...(((((((((((....)))))..)))))).........)))))))) ( -35.00)
>DroEre_CAF1 6092 120 - 1
GGACCCGUCUUCAAGGGCACUGGGCUCCAAGCAAAAUGGUUUUACCAUGGCAGUAAUGGCGGAAAAUUAUCCCGAUUGCGUGCUCACUAAUAAGCAACUGCAUGAGAUCGAAGACGGUCU
(((((.((((((..((((((..........((...((((.....)))).)).(((((.(.(((......)))).)))))))))))........((....))........))))))))))) ( -42.50)
>DroYak_CAF1 6055 120 - 1
AGAGCCGUCUUCACGGGCACUAAGCACGAAGCAGAAUGGUCUUACCAUGGCAAUUAUGGCAGAAACUUAUCCGGAUUGCUUGCUGACUAAUAAGCAACUGCAUGAGAUCGAAGACGGCUU
.(((((((((((.((.((.....)).))..((((.((((.....))))(((((((.(((.(........)))))))))))((((........)))).))))........))))))))))) ( -42.10)
>consensus
AGAGCCGUC___AUGGG______CCUCCAAGCAGAAUAGUAUUACCAUGGCAGUAAUGGCGGAAAAUUAUCCGGAUUGCGAGCUGACUAAUCAGCAAUUGCAUGAGAUCGAAGCCGGCCU
...((((.....................................((((.......))))((((......))))(((((((((((((....)))))..)))))....))).....)))).. (-16.14 = -17.74 +   1.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:55 2006