Locus 6481

Sequence ID	2L_DroMel_CAF1
Location	18,200,594 – 18,200,739
Length	145
Max. P	0.760213

overview

Window 3

Location	18,200,594 – 18,200,689
Length	95
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	80.87
Mean single sequence MFE	-35.58
Consensus MFE	-22.01
Energy contribution	-23.17
Covariance contribution	1.16
Combinations/Pair	1.10
Mean z-score	-1.74
Structure conservation index	0.62
SVM decision value	0.07
SVM RNA-class probability	0.569151
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18200594 95 + 22407834
------GCU-CGCAUUGCUGUUGCUG---------CUGCUGUGAUUGCUGGUCGUGGUGCACUUGAGCAAUGUGGCAGUGCACUCAUCCAAUGCAGACUUAGUGCACUCCU
------((.-(((((((((...(.((---------(.((..((((.....))))..))))))...)))))))))))((((((((..((.......))...))))))))... ( -35.40)
>DroVir_CAF1 66465 102 + 1
GAUCCGGCUUGGCAUUGCUGUUGCUGCCGCCGCCGCC---------GCCGCUGUUUGCGCACUUCAGCAAUGUGGCCGCGCAUUCGUCCAGAGCCGUUUUGGUGCAAUCCU
((..((((((((((..((....))))))...((.((.---------(((((...((((........)))).))))).)))).........))))))..))((......)). ( -36.30)
>DroSec_CAF1 43562 95 + 1
------GCU-CGCAUUGCUGUUGCUG---------CUGCUGUGAUUGCUGGUCGUGGUGCACUUGAGCAAUGUGGCAGUGCACUCAUCCAAUGCAGACUUAGUGCACUCCU
------((.-(((((((((...(.((---------(.((..((((.....))))..))))))...)))))))))))((((((((..((.......))...))))))))... ( -35.40)
>DroSim_CAF1 44171 95 + 1
------GCU-CGCAUUGCUGUUGCUG---------CUGCUGUGAUUGCUGGUCGUGGUGCACUUGAGCAAUGUGGCAGUGCACUCAUCCAACGCAGACUUAGUGCACUCCU
------((.-(((((((((...(.((---------(.((..((((.....))))..))))))...)))))))))))((((((((..((.......))...))))))))... ( -35.40)
>DroEre_CAF1 43745 95 + 1
------GCU-UGCAUUGCUGUUGCUG---------CUGCUGUGAUUGCUGGUCGUGGUGCACUUGAGCAAUGUGGCAGUGCACUCGUCCAAUGCAGACUUGGUGCACUCUU
------(((-.((((((((...(.((---------(.((..((((.....))))..))))))...)))))))))))((((((((.(((.......)))..))))))))... ( -35.40)
>consensus
______GCU_CGCAUUGCUGUUGCUG_________CUGCUGUGAUUGCUGGUCGUGGUGCACUUGAGCAAUGUGGCAGUGCACUCAUCCAAUGCAGACUUAGUGCACUCCU
......(((..((((((((..(((.............((..((((.....))))..)))))....)))))))))))((((((((.(..(......)..).))))))))... (-22.01 = -23.17 +   1.16)

alignment

secondary structure

dotplot

Window 4

Location	18,200,615 – 18,200,719
Length	104
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	83.09
Mean single sequence MFE	-37.07
Consensus MFE	-25.17
Energy contribution	-25.48
Covariance contribution	0.31
Combinations/Pair	1.27
Mean z-score	-2.02
Structure conservation index	0.68
SVM decision value	0.19
SVM RNA-class probability	0.625719
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18200615 104 - 22407834
UGGCGCAGCUGUGCAGCAGCGAUCUGUUGCAGGAGUGCACUAAGUCUGCAUUGGAUGAGUGCACUGCCACAUUGCUCAAGUGCACCACGACCAGC------AAUCACAGC
.......((((((((((((....))))))).((((((((((..((((.....)))).)))))))).))..((((((...(((...)))....)))------))).))))) ( -38.50)
>DroPse_CAF1 47203 110 - 1
UGGCUCAAUUGUGCAGCAGCGAUCUGUUGCAGGAGUGCACCAAAUCCGCACUGGACGAGUGCACGGCCACACUGCUCCAGUGCACCACCACCAGCACCGCCAAUCAGAGC
((((....((.((((((((....)))))))).))((((.........((((((((..((((........))))..))))))))..........)))).))))........ ( -40.21)
>DroSim_CAF1 44192 104 - 1
UGGCGCAGCUGUGCAGCAGCGAUCUGUUGCAGGAGUGCACUAAGUCUGCGUUGGAUGAGUGCACUGCCACAUUGCUCAAGUGCACCACGACCAGC------AAUCACAGC
.......((((((((((((....))))))).((((((((((..((((.....)))).)))))))).))..((((((...(((...)))....)))------))).))))) ( -38.50)
>DroEre_CAF1 43766 104 - 1
UGUCGCAGCUGUGCAGCAGCGAUCUGUUGCAAGAGUGCACCAAGUCUGCAUUGGACGAGUGCACUGCCACAUUGCUCAAGUGCACCACGACCAGC------AAUCACAGC
.......((((((((((((....)))))))...(((((((...((((.....))))..))))))).....((((((...(((...)))....)))------))).))))) ( -36.00)
>DroWil_CAF1 66886 101 - 1
UGGCUCAAUUGUGUAGCAGUGAUCUGUUACAAGAUUGCACUAAAUCAGCUUUAGAUGAAUGCACUGCCACGCUAUUGCAAUGCACCA---CCAGC------AAUGGCAGC
((((.(((((.((((((((....)))))))).)))))(((((((.....))))).))........)))).((((((((.........---...))------))))))... ( -30.90)
>DroPer_CAF1 47032 110 - 1
UGGCUCAAUUGUGCAGCAGCGAUCUGUUGCAGGAGUGCACCAAAUCCGCACUGAACGAGUGCACGGUCACACUGCUCCAGUGCACCACCACCAGCACCGCCAAUCAGAGC
((((....((.((((((((....)))))))).))((((.........(((((.....)))))..(((..(((((...))))).))).......)))).))))........ ( -38.30)
>consensus
UGGCGCAACUGUGCAGCAGCGAUCUGUUGCAGGAGUGCACCAAAUCUGCAUUGGACGAGUGCACUGCCACACUGCUCAAGUGCACCACGACCAGC______AAUCACAGC
(((((......((((((((....))))))))...((((((...((((.....))))..)))))))))))...(((......))).......................... (-25.17 = -25.48 +   0.31)

alignment

secondary structure

dotplot

Window 5

Location	18,200,649 – 18,200,739
Length	90
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	68.49
Mean single sequence MFE	-35.10
Consensus MFE	-16.54
Energy contribution	-16.68
Covariance contribution	0.14
Combinations/Pair	1.50
Mean z-score	-1.66
Structure conservation index	0.47
SVM decision value	0.50
SVM RNA-class probability	0.760213
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18200649 90 - 22407834
------------AAGCAGC---CACAAUAACAACU------------UGGCGCAGCUGUGCAGCAGCGAUCUGUUGCAGGAGUGCACUAAGUCUGCAUUGGAUGAGUGCACUGCCAC
------------.(((.((---((...........------------))))...))).((((((((....))))))))((((((((((..((((.....)))).)))))))).)).. ( -34.90)
>DroVir_CAF1 66527 105 - 1
AUUGCC------------CAAGAGCAACAACAAUCUGGCCCUGGGUAUGGCACAGCUGUGCAACGGCGAUCUGCUUGAGGAUUGCACCAAAACGGCUCUGGACGAAUGCGCGGCCAC
.((((.------------.....))))........(((((.((.((.((.((.((((((......(((((((......)))))))......)))))).))..)).)).)).))))). ( -33.60)
>DroPse_CAF1 47243 102 - 1
GUUGACCUUCUCGGGCAGC---CACAACAACAAUC------------UGGCUCAAUUGUGCAGCAGCGAUCUGUUGCAGGAGUGCACCAAAUCCGCACUGGACGAGUGCACGGCCAC
((((.(((....)))))))---.............------------(((((...((.((((((((....)))))))).))((((((....(((.....)))...))))))))))). ( -35.60)
>DroSim_CAF1 44226 90 - 1
------------AAGCAGC---CACAACAACAACU------------UGGCGCAGCUGUGCAGCAGCGAUCUGUUGCAGGAGUGCACUAAGUCUGCGUUGGAUGAGUGCACUGCCAC
------------.(((.((---((...........------------))))...))).((((((((....))))))))((((((((((..((((.....)))).)))))))).)).. ( -34.90)
>DroMoj_CAF1 68610 117 - 1
GUUGCCAUUAGCUGUCAACAAGAGCAACAACAAUUUGGCAAUGGGCAUGGCUCAGCUGUGCAGCAGCGAUCUGCUAGAGGACUGCACCAAGACGGCGCUCGAUGAUUGUGCAGCGAC
(((((.....((((((.................(((((((.(((((...)))))((((.....))))....)))))))((......))..))))))((.(((...))).)).))))) ( -35.50)
>DroPer_CAF1 47072 102 - 1
GUUGACCUUCUCGGGCAGC---CACAACAACAAUC------------UGGCUCAAUUGUGCAGCAGCGAUCUGUUGCAGGAGUGCACCAAAUCCGCACUGAACGAGUGCACGGUCAC
..(((((.....(((((((---((...........------------))))....((.((((((((....)))))))).)).))).))......(((((.....)))))..))))). ( -36.10)
>consensus
GUUG_C______AGGCAGC___CACAACAACAAUC____________UGGCUCAGCUGUGCAGCAGCGAUCUGUUGCAGGAGUGCACCAAAUCCGCACUGGACGAGUGCACGGCCAC
......................................................(((((((((((((.....)))))...(((((.........))))).......))))))))... (-16.54 = -16.68 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:14 2006