Locus 2467

Sequence ID	2R_DroMel_CAF1
Location	8,859,316 – 8,859,440
Length	124
Max. P	0.990397

overview

Window 3

Location	8,859,316 – 8,859,418
Length	102
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	75.28
Mean single sequence MFE	-23.22
Consensus MFE	-16.77
Energy contribution	-17.30
Covariance contribution	0.53
Combinations/Pair	1.06
Mean z-score	-1.05
Structure conservation index	0.72
SVM decision value	0.48
SVM RNA-class probability	0.753097
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8859316 102 + 20766785
AGCACA--CACAUACACACGCUCAAAGAAUGUGUAAGUGCAAAAGGCAUUUAUU----UCUGGACCCAAAUGAAGGCACGACCAGGCGUGGCUUCAAAUUGUAAUGAU
.((...--(((.((((((..(.....)..)))))).)))......)).......----............(((((.((((......)))).)))))............ ( -24.00)
>DroSec_CAF1 104200 79 + 1
AGC-------------------------AUGUGUAAGUGCAAAAGGCAUUUAUU----UCUGGACCCAAAUGAAGGCACGACCAGGCGUGGCUUCAAAUUGUAAUGAU
..(-------------------------(...((((((((.....)))))))).----..))........(((((.((((......)))).)))))............ ( -20.60)
>DroSim_CAF1 104116 79 + 1
AGC-------------------------AUGUGUAAGUGCAAAAGGCAUUUAUU----UCUGGACCCAAAUGAAGGCACGACCAGGCGUGGCUUCAAAUUGUAAUGAU
..(-------------------------(...((((((((.....)))))))).----..))........(((((.((((......)))).)))))............ ( -20.60)
>DroEre_CAF1 105864 99 + 1
-----ACACACACACACGCACUCAAAGGCUGUGUAAGUGCAAAAGGCAUUUAUA----UCUGGACCCAAAUGAUGGCACGACCAGGCGUGGCUUCAAAUUGUAAUGAU
-----.........(((((...........((((((((((.....)))))))))----)((((..(((.....))).....))))))))).................. ( -23.40)
>DroYak_CAF1 108186 104 + 1
GGCACACAAACACACACUCACUCAAAGGCUGUGUAAGUGCAAAAGGCAUUUAUU----UCUGGACCCAAAUGAUGGCACGACCAGGCGUGGCUUCAAAUUGUAAUGAU
(((.(((..(((((..((.......))..)))))((((((.....))))))...----(((((..(((.....))).....))))).))))))............... ( -20.80)
>DroPer_CAF1 119690 94 + 1
GGCAUUCAAAUAC--UC------------CCUGUAAGUGCAAAAGGCAUUUAUCCGGACCCGGACCUCAUUGCAGGCACUGCCAGGCGUGGCUCCGGAUUGUAAUGAU
..(((((((....--((------------(..((((((((.....))))))))..))).(((((((....(((.(((...)))..))).)).))))).))).)))).. ( -29.90)
>consensus
AGC__A___ACAC__AC___________AUGUGUAAGUGCAAAAGGCAUUUAUU____UCUGGACCCAAAUGAAGGCACGACCAGGCGUGGCUUCAAAUUGUAAUGAU
................................((((((((.....)))))))).................(((((.((((......)))).)))))............ (-16.77 = -17.30 +   0.53)

alignment

secondary structure

dotplot

Window 4

Location	8,859,346 – 8,859,440
Length	94
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	87.80
Mean single sequence MFE	-29.88
Consensus MFE	-27.69
Energy contribution	-28.05
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-2.27
Structure conservation index	0.93
SVM decision value	2.21
SVM RNA-class probability	0.990397
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8859346 94 + 20766785
GUAAGUGCAAAAGGCAUUUAUUUCUGGACCCAAAUGAAGGCACGACCAGGCGUGGCUUCAAAUUGUAAUGAUGCCACGCCCCC----------------ACACCCAUAGC
((((((((.....))))))))...(((...........((.....)).((((((((.(((........))).))))))))...----------------....))).... ( -28.80)
>DroSec_CAF1 104207 93 + 1
GUAAGUGCAAAAGGCAUUUAUUUCUGGACCCAAAUGAAGGCACGACCAGGCGUGGCUUCAAAUUGUAAUGAUGCCACGCC-CC----------------ACACCCAACGC
((((((((.....))))))))...(((...........((.....)).((((((((.(((........))).))))))))-..----------------....))).... ( -29.00)
>DroSim_CAF1 104123 94 + 1
GUAAGUGCAAAAGGCAUUUAUUUCUGGACCCAAAUGAAGGCACGACCAGGCGUGGCUUCAAAUUGUAAUGAUGCCACGCCCCC----------------ACACCCAACGC
((((((((.....))))))))...(((...........((.....)).((((((((.(((........))).))))))))...----------------....))).... ( -29.00)
>DroEre_CAF1 105891 110 + 1
GUAAGUGCAAAAGGCAUUUAUAUCUGGACCCAAAUGAUGGCACGACCAGGCGUGGCUUCAAAUUGUAAUGAUGCCACGCCCCCACGGCCCCACUCCCCCACGCCCAUGGC
((((((((.....))))))))...(((..((......(((.....)))((((((((.(((........))).)))))))).....))..))).........(((...))) ( -34.40)
>DroYak_CAF1 108218 101 + 1
GUAAGUGCAAAAGGCAUUUAUUUCUGGACCCAAAUGAUGGCACGACCAGGCGUGGCUUCAAAUUGUAAUGAUGCCACGCCCCCACG---------CCCCACGCCCAUCGC
((((((((.....))))))))..............(((((........((((((((.(((........))).)))))))).....(---------(.....))))))).. ( -32.20)
>DroAna_CAF1 103701 93 + 1
-U-UAUGCUAAAGGCAUUUAUUUCUGGACCCAAAUGAAGGCACGACCAGGCGUGGCUUCAAAUUGUAAUGAUGCCACGCCCCCUC---------------CACCCACCAC
-.-.((((.....)))).......((((..........((.....)).((((((((.(((........))).))))))))...))---------------))........ ( -25.90)
>consensus
GUAAGUGCAAAAGGCAUUUAUUUCUGGACCCAAAUGAAGGCACGACCAGGCGUGGCUUCAAAUUGUAAUGAUGCCACGCCCCC________________ACACCCAUCGC
((((((((.....))))))))...(((...........((.....)).((((((((.(((........))).)))))))).......................))).... (-27.69 = -28.05 +   0.36)

alignment

secondary structure

dotplot

Window 5

Location	8,859,346 – 8,859,440
Length	94
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	87.80
Mean single sequence MFE	-38.97
Consensus MFE	-32.74
Energy contribution	-33.05
Covariance contribution	0.31
Combinations/Pair	1.08
Mean z-score	-2.99
Structure conservation index	0.84
SVM decision value	1.61
SVM RNA-class probability	0.967249
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8859346 94 - 20766785
GCUAUGGGUGU----------------GGGGGCGUGGCAUCAUUACAAUUUGAAGCCACGCCUGGUCGUGCCUUCAUUUGGGUCCAGAAAUAAAUGCCUUUUGCACUUAC
((...((((((----------------..(((((((((.(((........))).)))))))))....(..(((......)))..)........))))))...))...... ( -35.10)
>DroSec_CAF1 104207 93 - 1
GCGUUGGGUGU----------------GG-GGCGUGGCAUCAUUACAAUUUGAAGCCACGCCUGGUCGUGCCUUCAUUUGGGUCCAGAAAUAAAUGCCUUUUGCACUUAC
(((..((((((----------------.(-((((((((.(((........))).)))))))))....(..(((......)))..)........))))))..)))...... ( -37.00)
>DroSim_CAF1 104123 94 - 1
GCGUUGGGUGU----------------GGGGGCGUGGCAUCAUUACAAUUUGAAGCCACGCCUGGUCGUGCCUUCAUUUGGGUCCAGAAAUAAAUGCCUUUUGCACUUAC
(((..((((((----------------..(((((((((.(((........))).)))))))))....(..(((......)))..)........))))))..)))...... ( -37.00)
>DroEre_CAF1 105891 110 - 1
GCCAUGGGCGUGGGGGAGUGGGGCCGUGGGGGCGUGGCAUCAUUACAAUUUGAAGCCACGCCUGGUCGUGCCAUCAUUUGGGUCCAGAUAUAAAUGCCUUUUGCACUUAC
((...((((((.((((((((((((((...(((((((((.(((........))).)))))))))...)).))).))))))...)))........))))))...))...... ( -44.30)
>DroYak_CAF1 108218 101 - 1
GCGAUGGGCGUGGGG---------CGUGGGGGCGUGGCAUCAUUACAAUUUGAAGCCACGCCUGGUCGUGCCAUCAUUUGGGUCCAGAAAUAAAUGCCUUUUGCACUUAC
((((.((((((((.(---------((...(((((((((.(((........))).)))))))))...))).))))..((((....)))).......)))).))))...... ( -45.60)
>DroAna_CAF1 103701 93 - 1
GUGGUGGGUG---------------GAGGGGGCGUGGCAUCAUUACAAUUUGAAGCCACGCCUGGUCGUGCCUUCAUUUGGGUCCAGAAAUAAAUGCCUUUAGCAUA-A-
((...((((.---------------((..(((((((((.(((........))).)))))))))..))(..(((......)))..)..........))))...))...-.- ( -34.80)
>consensus
GCGAUGGGUGU________________GGGGGCGUGGCAUCAUUACAAUUUGAAGCCACGCCUGGUCGUGCCUUCAUUUGGGUCCAGAAAUAAAUGCCUUUUGCACUUAC
((...((((((..................(((((((((.(((........))).)))))))))....(..(((......)))..)........))))))...))...... (-32.74 = -33.05 +   0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:47 2006