Locus 6564

Sequence ID	3L_DroMel_CAF1
Location	17,378,150 – 17,378,359
Length	209
Max. P	0.952472

overview

Window 6

Location	17,378,150 – 17,378,247
Length	97
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	95.08
Mean single sequence MFE	-21.18
Consensus MFE	-18.22
Energy contribution	-19.02
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.27
Structure conservation index	0.86
SVM decision value	0.07
SVM RNA-class probability	0.566503
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17378150 97 + 23771897
CUGAUCAUUCCACCUUUUGGUAAUAAAGUUUUUUAGCUGAAAUUAUCAAGGGUUCACUUCCAAGGAAGCUCCGAGAAUCAACUGCU-UGGCACUCAUU
...........((((((.((((((..((((....))))...))))))))))))...((((....))))....(((..((((....)-)))..)))... ( -18.60)
>DroSec_CAF1 5061 97 + 1
CUGAUCAUUCCACCUUUUGGUAAUAAAGUUUUUUAGCUGAAAUUAUCAAGGGUUCACUUCCAAGGAAGCCCCGAGAAUCAACUGCU-UGGCAGUCAUU
.(((((..........((((((((..((((....))))...))))))))(((....((((....)))).)))..).))))(((((.-..))))).... ( -21.30)
>DroSim_CAF1 4766 97 + 1
CUGAUCAUUCCACCUUUUGGUAAUAAAGUUUUUUAGCUGAAAUUAUCAAGGGUUCACUUCCAAGGAAGCCCCGAGAAUCAACUGCU-UGGCAGUCAUU
.(((((..........((((((((..((((....))))...))))))))(((....((((....)))).)))..).))))(((((.-..))))).... ( -21.30)
>DroEre_CAF1 5161 95 + 1
CUGAUCAUUCCACCU-CUGGUAAUAAAGUU-UUUAGCUGAAAUUAUCAAGGGUUCACUUCCAAGGAAAC-CCGAGAAUCAACUGCUUUGGCAGCCAUU
.............((-((((((((..(((.-....)))...))))))).(((((..((....))..)))-)))))......((((....))))..... ( -21.90)
>DroYak_CAF1 6038 96 + 1
CUGAUCAUUCCACCU-UUGGUAAUAAAGUUUUUUAGCUGAAAUUAUCAAGGGUUCACUUCCAAGGAAAC-CCGAGAUUCAACUGCUUUGGCAGCCAUU
..((((.........-((((((((..((((....))))...))))))))(((((..((....))..)))-))..))))...((((....))))..... ( -22.80)
>consensus
CUGAUCAUUCCACCUUUUGGUAAUAAAGUUUUUUAGCUGAAAUUAUCAAGGGUUCACUUCCAAGGAAGC_CCGAGAAUCAACUGCU_UGGCAGUCAUU
.(((((.....((((.((((((((..((((....))))...))))))))))))...((((....))))......)).))).((((....))))..... (-18.22 = -19.02 +   0.80)

alignment

secondary structure

dotplot

Window 7

Location	17,378,208 – 17,378,326
Length	118
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	90.63
Mean single sequence MFE	-29.14
Consensus MFE	-23.96
Energy contribution	-24.32
Covariance contribution	0.36
Combinations/Pair	1.14
Mean z-score	-1.94
Structure conservation index	0.82
SVM decision value	1.42
SVM RNA-class probability	0.952472
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17378208 118 + 23771897
UCCAAGGAAGCUCCGAGAAUCAACUGCU-UGGCACUCAUUAUUUUUAAUGGAAAAGCAAAUGGAUGAAUGAAUCUGGCAUUAUUUAUGAAGGCUUCCCAUAUGGAAAGCUUACAAAACA
((((.(((((((.......(((..((((-(.....((((((....))))))..)))))..)))((((((((........))))))))...)))))))....)))).............. ( -25.10)
>DroSec_CAF1 5119 118 + 1
UCCAAGGAAGCCCCGAGAAUCAACUGCU-UGGCAGUCAUUAUUUUUAAUGGAAAAGCAAAUGGAUGGAUGAAUCUGGCAUUAUAUAUGAAGGCUUCCCAUAUGGGAAGCUUACAAAACA
.........(((............((((-(.....((((((....))))))..)))))...((((......)))))))........((.(((((((((....))))))))).))..... ( -31.10)
>DroSim_CAF1 4824 118 + 1
UCCAAGGAAGCCCCGAGAAUCAACUGCU-UGGCAGUCAUUAUUUUUAAUGGAAAAGCAAAUGGAUGGAUGAAUCUGGCAUUAUAUAUGAAGGCUUCCCAUAUGGGAAGCUUACAAAACA
.........(((............((((-(.....((((((....))))))..)))))...((((......)))))))........((.(((((((((....))))))))).))..... ( -31.10)
>DroEre_CAF1 5217 117 + 1
UCCAAGGAAAC-CCGAGAAUCAACUGCUUUGGCAGCCAUUAUUUUUAAUGGAAAAGCAAAUGGAUGGAUGUAUCUAACAUUAUUCA-AAUGGCUUUCCUUAUGGGAAGCUUACGAAACA
((((.((....-))..........((((((.....((((((....)))))).))))))..))))..(((((.....))))).(((.-...((((((((....))))))))...)))... ( -30.90)
>DroYak_CAF1 6095 117 + 1
UCCAAGGAAAC-CCGAGAUUCAACUGCUUUGGCAGCCAUUAUUUUUAAUGGAAAAGCAAAUGGAUGGAUGAAUCUGGCAUUAUUCA-AAUAGCUUUCCUCAUGGCAAGCUUACAAAACA
(((..((....-))...(((((..((((((.....((((((....)))))).))))))..))))))))(((((........)))))-...(((((.((....)).)))))......... ( -27.50)
>consensus
UCCAAGGAAGC_CCGAGAAUCAACUGCU_UGGCAGUCAUUAUUUUUAAUGGAAAAGCAAAUGGAUGGAUGAAUCUGGCAUUAUUUAUGAAGGCUUCCCAUAUGGGAAGCUUACAAAACA
((((.((.....)).........((((....))))((((((....)))))).........))))..((((.......))))........(((((((((....)))))))))........ (-23.96 = -24.32 +   0.36)

alignment

secondary structure

dotplot

Window 8

Location	17,378,247 – 17,378,359
Length	112
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	91.69
Mean single sequence MFE	-19.44
Consensus MFE	-17.12
Energy contribution	-17.16
Covariance contribution	0.04
Combinations/Pair	1.25
Mean z-score	-1.23
Structure conservation index	0.88
SVM decision value	0.15
SVM RNA-class probability	0.606156
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17378247 112 - 23771897
GACCUUCAAUAACUGAUUGAUCUGCCCGUUCUUUGUUUUGUAAGCUUUCCAUAUGGGAAGCCUUCAUAAAUAAUGCCAGAUUCAUUCAUCCAUUUGCUUUUCCAUUAAAAAU
.............(((.(((((((...((...((((((((...(((((((....)))))))...)).)))))).)))))).))).)))........................ ( -20.20)
>DroSec_CAF1 5158 112 - 1
GACCUUCAAUAACUGAUUGAUCUGCCCGUUCUUUGUUUUGUAAGCUUCCCAUAUGGGAAGCCUUCAUAUAUAAUGCCAGAUUCAUCCAUCCAUUUGCUUUUCCAUUAAAAAU
..............(((.((((((...((...((((..((...(((((((....)))))))...))...)))).)))))))).))).......................... ( -21.60)
>DroSim_CAF1 4863 112 - 1
GACCUUCAGUAACUGAUUGAUCUGCCCGUUCUUUGUUUUGUAAGCUUCCCAUAUGGGAAGCCUUCAUAUAUAAUGCCAGAUUCAUCCAUCCAUUUGCUUUUCCAUUAAAAAU
..............(((.((((((...((...((((..((...(((((((....)))))))...))...)))).)))))))).))).......................... ( -21.60)
>DroEre_CAF1 5256 111 - 1
GACCUUCAAUCACUGAUUGAUCUGCUCGCUCUUUGUUUCGUAAGCUUCCCAUAAGGAAAGCCAUU-UGAAUAAUGUUAGAUACAUCCAUCCAUUUGCUUUUCCAUUAAAAAU
.....((((((...))))))...(((..(..........)..))).........((((((.((..-((.((.((((.....))))..)).))..)).))))))......... ( -16.50)
>DroYak_CAF1 6134 111 - 1
GACCUUCAAUAACUGAUUGAUCUGCCCGUUCUUUGUUUUGUAAGCUUGCCAUGAGGAAAGCUAUU-UGAAUAAUGCCAGAUUCAUCCAUCCAUUUGCUUUUCCAUUAAAAAU
..............(((.((((((...((...((((((....(((((.((....)).)))))...-.)))))).)))))))).))).......................... ( -17.30)
>consensus
GACCUUCAAUAACUGAUUGAUCUGCCCGUUCUUUGUUUUGUAAGCUUCCCAUAUGGGAAGCCUUCAUAAAUAAUGCCAGAUUCAUCCAUCCAUUUGCUUUUCCAUUAAAAAU
..............(((.((((((...((...((((((.....(((((((....)))))))......)))))).)))))))).))).......................... (-17.12 = -17.16 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:29 2006