Locus 1962

Sequence ID	2L_DroMel_CAF1
Location	5,309,916 – 5,310,058
Length	142
Max. P	0.998994

overview

Window 5

Location	5,309,916 – 5,310,020
Length	104
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	89.26
Mean single sequence MFE	-33.65
Consensus MFE	-30.40
Energy contribution	-31.40
Covariance contribution	1.00
Combinations/Pair	1.07
Mean z-score	-1.67
Structure conservation index	0.90
SVM decision value	0.77
SVM RNA-class probability	0.847284
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5309916 104 - 22407834
UUCGGGCCACAGGGUCUUGUGUCAAAUCCUUGUGGUCCAGACCUGGCCCUAGAGUUCUACAUAGAGAUGGAGACAUGCAUGCAUCGGUAUCUAAUAGUUAUCAC
...(((((((((((..(((...)))..)))))))))))..(((..((.......((((....))))(((....)))....))...)))................ ( -29.90)
>DroSec_CAF1 85620 104 - 1
UUUGGUCCACAGGGCCUGGAGUCCAGUCCCUGUGGUCCAGACCUGGCCCUAGAGUUCUACAUAGAGAUGGAGACAUGCAUGCAUCGGUAUCUUAUAGUAAACAC
(((((.((((((((.((((...)))).)))))))).)))))............(((.(((...((((((..((..((....))))..))))))...)))))).. ( -35.80)
>DroSim_CAF1 89427 103 - 1
UUUGGGCCACAGGGCCUGGAGUCCAGUCCCUGUGGUCCAGACCUGGCCCUAGAGUUCUAC-UAGAGAUGGAGACAUGCAUGCAUUGGUAUCUUAUAGUAAACAC
.(((((((((((((.((((...)))).)))))))))))))(((..((.((((.......)-)))..(((....)))....))...)))................ ( -41.20)
>DroYak_CAF1 90376 102 - 1
UUUAGGCCACAGGGUCU--AUCCGAGUCCUUGUGGUCCAGACCUGGCCCUAGCGUUCUACACAGAGAUGGAGACAAGCAUGCAUCGGUAUCUAAUAGUAAACAC
....((((((((((.((--.....)).)))))))))).(((....(((...(((((((......)))((....))...))))...))).)))............ ( -27.70)
>consensus
UUUGGGCCACAGGGCCUGGAGUCCAGUCCCUGUGGUCCAGACCUGGCCCUAGAGUUCUACAUAGAGAUGGAGACAUGCAUGCAUCGGUAUCUAAUAGUAAACAC
.(((((((((((((.(((.....))).)))))))))))))(((..((.......((((....))))(((....)))....))...)))................ (-30.40 = -31.40 +   1.00)

alignment

secondary structure

dotplot

Window 6

Location	5,309,940 – 5,310,058
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	81.41
Mean single sequence MFE	-39.03
Consensus MFE	-23.86
Energy contribution	-25.96
Covariance contribution	2.10
Combinations/Pair	1.18
Mean z-score	-2.90
Structure conservation index	0.61
SVM decision value	2.01
SVM RNA-class probability	0.985602
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5309940 118 + 22407834
AUGCAUGUCUCCAUCUCUAUGUAGAACUCUAGGGCCAGGUCUGGACCACAAGGAUUUGACACAAGACCCUGUGGCCCGAAACUGGCCAACACUUAUCUGUGUGUAUGUUUAUCUAUCC
.((((((..........))))))((((.....((((((...(((.(((((.((.((((...)))).)).))))).)))...)))))).((((......))))....))))........ ( -34.50)
>DroSec_CAF1 85644 118 + 1
AUGCAUGUCUCCAUCUCUAUGUAGAACUCUAGGGCCAGGUCUGGACCACAGGGACUGGACUCCAGGCCCUGUGGACCAAAACUGUCCAACACGUAUCCGUGUGUAUGUUUAUCUAUCC
.((((((..........))))))((((....((((.((...(((.((((((((.((((...)))).)))))))).)))...)))))).(((((....)))))....))))........ ( -40.80)
>DroSim_CAF1 89451 117 + 1
AUGCAUGUCUCCAUCUCUA-GUAGAACUCUAGGGCCAGGUCUGGACCACAGGGACUGGACUCCAGGCCCUGUGGCCCAAAACUGGCCAACACGUAUCCGUGUGUAUGUUUAUCUAUCC
..(((((.........(((-(.......))))((((((...(((.((((((((.((((...)))).)))))))).)))...)))))).(((((....))))).))))).......... ( -48.20)
>DroEre_CAF1 83126 90 + 1
AUGCUUGUCUCCAUCUCUAUGUAU-------GGGCCAGGUCUGGACCAUAAGGAC---------------------UAGACCUGGCCAAAACGUAUCUGUGUGUAUGUGUAUCUAUCC
((((.......(((...(((((..-------.((((((((((((.((....)).)---------------------)))))))))))...)))))...))).......))))...... ( -32.54)
>DroYak_CAF1 90400 116 + 1
AUGCUUGUCUCCAUCUCUGUGUAGAACGCUAGGGCCAGGUCUGGACCACAAGGACUCGGAU--AGACCCUGUGGCCUAAACCUGGCCAAGACGUAUCCGUGUGUAUGUUUAUCUAUCC
..((...(((.(((....))).)))..))(((((((((((.(((.(((((.((.((.....--)).)).))))).))).)))))))).((((((((......))))))))..)))... ( -39.10)
>consensus
AUGCAUGUCUCCAUCUCUAUGUAGAACUCUAGGGCCAGGUCUGGACCACAAGGACUGGACUC_AGACCCUGUGGCCCAAAACUGGCCAACACGUAUCCGUGUGUAUGUUUAUCUAUCC
((((............................((((((...(((.(((((.((.(((.....))).)).))))).)))...)))))).(((((....)))))))))............ (-23.86 = -25.96 +   2.10)

alignment

secondary structure

dotplot

Window 7

Location	5,309,940 – 5,310,058
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	81.41
Mean single sequence MFE	-43.78
Consensus MFE	-31.88
Energy contribution	-36.30
Covariance contribution	4.42
Combinations/Pair	1.09
Mean z-score	-3.69
Structure conservation index	0.73
SVM decision value	3.32
SVM RNA-class probability	0.998994
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5309940 118 - 22407834
GGAUAGAUAAACAUACACACAGAUAAGUGUUGGCCAGUUUCGGGCCACAGGGUCUUGUGUCAAAUCCUUGUGGUCCAGACCUGGCCCUAGAGUUCUACAUAGAGAUGGAGACAUGCAU
...((((.........((((......)))).((((((.(..(((((((((((..(((...)))..)))))))))))..).)))))).......)))).......(((....))).... ( -41.50)
>DroSec_CAF1 85644 118 - 1
GGAUAGAUAAACAUACACACGGAUACGUGUUGGACAGUUUUGGUCCACAGGGCCUGGAGUCCAGUCCCUGUGGUCCAGACCUGGCCCUAGAGUUCUACAUAGAGAUGGAGACAUGCAU
...((((.........(((((....))))).((.(((.(((((.((((((((.((((...)))).)))))))).))))).)))..))......)))).......(((....))).... ( -45.80)
>DroSim_CAF1 89451 117 - 1
GGAUAGAUAAACAUACACACGGAUACGUGUUGGCCAGUUUUGGGCCACAGGGCCUGGAGUCCAGUCCCUGUGGUCCAGACCUGGCCCUAGAGUUCUAC-UAGAGAUGGAGACAUGCAU
((.((((.........(((((....))))).((((((.((((((((((((((.((((...)))).)))))))))))))).)))))).......)))))-)....(((....))).... ( -56.40)
>DroEre_CAF1 83126 90 - 1
GGAUAGAUACACAUACACACAGAUACGUUUUGGCCAGGUCUA---------------------GUCCUUAUGGUCCAGACCUGGCCC-------AUACAUAGAGAUGGAGACAAGCAU
..........................((...((((((((((.---------------------(.((....)).).)))))))))).-------..)).......((....))..... ( -28.20)
>DroYak_CAF1 90400 116 - 1
GGAUAGAUAAACAUACACACGGAUACGUCUUGGCCAGGUUUAGGCCACAGGGUCU--AUCCGAGUCCUUGUGGUCCAGACCUGGCCCUAGCGUUCUACACAGAGAUGGAGACAAGCAU
....................(((.((((...((((((((((.((((((((((.((--.....)).)))))))))).))))))))))...))))))).........((....))..... ( -47.00)
>consensus
GGAUAGAUAAACAUACACACGGAUACGUGUUGGCCAGUUUUGGGCCACAGGGCCU_GAGUCCAGUCCUUGUGGUCCAGACCUGGCCCUAGAGUUCUACAUAGAGAUGGAGACAUGCAU
...((((.........(((((....))))).((((((.((((((((((((((.(((.....))).)))))))))))))).)))))).......))))........((....))..... (-31.88 = -36.30 +   4.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:16:05 2006