Locus 6334

Sequence ID	X_DroMel_CAF1
Location	15,991,432 – 15,991,692
Length	260
Max. P	0.857005

overview

Window 9

Location	15,991,432 – 15,991,552
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.99
Mean single sequence MFE	-29.38
Consensus MFE	-26.00
Energy contribution	-26.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.88
SVM decision value	0.81
SVM RNA-class probability	0.857005
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15991432 120 + 22224390
CAUCAACCGUCAACAUCGCGGCCCUGUCGCAUAAUAUGAUAAUAUGAUAAUAUGGCAAUCGCCCCAGGUAGAGACAACAAAGGGAUCUGUAUCUGUCCGCGACAGAUACAACUUCUACUA
..((.((((((......(((((...)))))...((((....))))))).....(((....)))...))).)).........((((..((((((((((...))))))))))..)))).... ( -30.70)
>DroSec_CAF1 59318 119 + 1
CAUCAACCGUCAACGACGCGGCCCUGUCGCAUAAUAUGAUAAUAUGAUAAUAUG-CAAUCGCCCCAGGUAGAGACAACAAAGGGAUCUGUAUCUGUCCGCGACAGAUACUACUUCUACUA
......((((.......))))((((((((((((.(((.((...)).))).))))-)..(((((...))).))))).....))))....(((((((((...)))))))))........... ( -28.60)
>DroSim_CAF1 50394 119 + 1
CAUCAACCGUCAACGACGCGGCCCUGUCGCAUAAUAUGAUAAUAUGAUAAUAUG-CAAUCGCCCCAGGUAGAGACAACAAAGGGAUCUGUAUCUGUCCGCGACAGAUACUACUUCUACUA
......((((.......))))((((((((((((.(((.((...)).))).))))-)..(((((...))).))))).....))))....(((((((((...)))))))))........... ( -28.60)
>DroEre_CAF1 58210 119 + 1
CAUCAACCGUCGACAUCGCGGCCCUGUCGCAUAAUAUGAUAAUAUGAUAAUAUG-CAAUCGCCCCAGGUAGAGACAACAAAGGGAUCUGUAUCUGUCCGCGACAGAUACUACUUCUACUA
......(((.((....)))))((((((((((((.(((.((...)).))).))))-)..(((((...))).))))).....))))....(((((((((...)))))))))........... ( -30.40)
>DroYak_CAF1 42420 119 + 1
CAUCAACCGUCAACAUCGCGGCCCUGUCGCAUAAUAUGAUAAUAUGAUAAUAUG-CAAUCGCCCCAGGUAGAGACAACAAAGGGAUCUGUAUCUGUCCGCGACAGAUACUACUUCUACUA
......((((.......))))((((((((((((.(((.((...)).))).))))-)..(((((...))).))))).....))))....(((((((((...)))))))))........... ( -28.60)
>consensus
CAUCAACCGUCAACAUCGCGGCCCUGUCGCAUAAUAUGAUAAUAUGAUAAUAUG_CAAUCGCCCCAGGUAGAGACAACAAAGGGAUCUGUAUCUGUCCGCGACAGAUACUACUUCUACUA
......((((.......))))..(((((((.......(((.((((....))))....)))....((((((.((((........).))).))))))...)))))))............... (-26.00 = -26.00 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	15,991,472 – 15,991,572
Length	100
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	92.75
Mean single sequence MFE	-26.90
Consensus MFE	-21.52
Energy contribution	-21.53
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.22
Structure conservation index	0.80
SVM decision value	0.75
SVM RNA-class probability	0.841928
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15991472 100 + 22224390
AAUAUGAUAAUAUGGCAAUCGCCCCAGGUAGAGACAACAAAGGGAUCUGUAUCUGUCCGCGACAGAUACAACUUCUACUAC--------CAACUCAACGGCGAAGGCG
..............((..(((((...(((((.(....)...((((..((((((((((...))))))))))..)))).))))--------)........)))))..)). ( -29.10)
>DroSec_CAF1 59358 99 + 1
AAUAUGAUAAUAUG-CAAUCGCCCCAGGUAGAGACAACAAAGGGAUCUGUAUCUGUCCGCGACAGAUACUACUUCUACUAC--------CAACUCAACGGCGAAGGCG
.............(-(..(((((...((((((((......((....))(((((((((...)))))))))....))).))))--------)........)))))..)). ( -27.60)
>DroSim_CAF1 50434 99 + 1
AAUAUGAUAAUAUG-CAAUCGCCCCAGGUAGAGACAACAAAGGGAUCUGUAUCUGUCCGCGACAGAUACUACUUCUACUAC--------CAACUCAACGGCGAAGGCG
.............(-(..(((((...((((((((......((....))(((((((((...)))))))))....))).))))--------)........)))))..)). ( -27.60)
>DroEre_CAF1 58250 104 + 1
AAUAUGAUAAUAUG-CAAUCGCCCCAGGUAGAGACAACAAAGGGAUCUGUAUCUGUCCGCGACAGAUACUACUUCUACUACAGUAAAACCAAGUAAACGGCGAAG---
..............-...(((((...(((((((.......((....))(((((((((...)))))))))...))))))).............(....))))))..--- ( -23.30)
>consensus
AAUAUGAUAAUAUG_CAAUCGCCCCAGGUAGAGACAACAAAGGGAUCUGUAUCUGUCCGCGACAGAUACUACUUCUACUAC________CAACUCAACGGCGAAGGCG
..................(((((......(((..(.......)..)))(((((((((...))))))))).............................)))))..... (-21.52 = -21.53 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	15,991,512 – 15,991,612
Length	100
Sequences	4
Columns	108
Reading direction	forward
Mean pairwise identity	88.94
Mean single sequence MFE	-32.62
Consensus MFE	-27.98
Energy contribution	-28.10
Covariance contribution	0.12
Combinations/Pair	1.00
Mean z-score	-1.55
Structure conservation index	0.86
SVM decision value	0.36
SVM RNA-class probability	0.705390
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15991512 100 + 22224390
AGGGAUCUGUAUCUGUCCGCGACAGAUACAACUUCUACUAC--------CAACUCAACGGCGAAGGCGAAAACGAAGGCGAAGGCGAAGGCGUUUGCGUGUCGAGCGA
.((((..((((((((((...))))))))))..)))).....--------...(((.(((((....))..........(((((.((....)).))))).))).)))... ( -34.30)
>DroSec_CAF1 59397 100 + 1
AGGGAUCUGUAUCUGUCCGCGACAGAUACUACUUCUACUAC--------CAACUCAACGGCGAAGGCGAAAACGAAGGCGAAGGCGAAGGCGUUUGCGUGUCGAGCGA
.((((...(((((((((...)))))))))...)))).....--------...(((.(((((....))..........(((((.((....)).))))).))).)))... ( -32.50)
>DroSim_CAF1 50473 100 + 1
AGGGAUCUGUAUCUGUCCGCGACAGAUACUACUUCUACUAC--------CAACUCAACGGCGAAGGCGAAAACGAAGGCGAAGGCGAAGGCGUUUGCGUGUCGAGCGA
.((((...(((((((((...)))))))))...)))).....--------...(((.(((((....))..........(((((.((....)).))))).))).)))... ( -32.50)
>DroEre_CAF1 58289 96 + 1
AGGGAUCUGUAUCUGUCCGCGACAGAUACUACUUCUACUACAGUAAAACCAAGUAAACGGCGAAG------------GCGAAGGCGAAGGCGUUUGCGUGUCGAGCGA
.((.....(((((((((...)))))))))((((........))))...)).......(((((...------------(((((.((....)).))))).)))))..... ( -31.20)
>consensus
AGGGAUCUGUAUCUGUCCGCGACAGAUACUACUUCUACUAC________CAACUCAACGGCGAAGGCGAAAACGAAGGCGAAGGCGAAGGCGUUUGCGUGUCGAGCGA
.((((...(((((((((...)))))))))...)))).....................(((((....((....))...(((((.((....)).))))).)))))..... (-27.98 = -28.10 +   0.12)

alignment

secondary structure

dotplot

Window 2

Location	15,991,572 – 15,991,692
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.53
Mean single sequence MFE	-31.54
Consensus MFE	-30.04
Energy contribution	-30.08
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.13
Structure conservation index	0.95
SVM decision value	0.36
SVM RNA-class probability	0.705200
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15991572 120 + 22224390
AAAACGAAGGCGAAGGCGAAGGCGUUUGCGUGUCGAGCGACAUCAUUUGCAUAACAAUGCUGGAGAUAGAGACGAUUCAAAUUUUUGGUCUCCCAGAGCAAUUUUCACGACGAUACGAUA
.........(((((.((....)).)))))((((((.((((......)))).......((((((((((.((((..........)))).))))))...))))..........)))))).... ( -34.10)
>DroSec_CAF1 59457 115 + 1
AAAACGAAGGCGAAGGCGAAGGCGUUUGCGUGUCGAGCGACAUCAUUUGCAUAACAAUGCUGGAGAUAGAGACGAUUCAAAUUUUUGGUCUCCCAGAGCAAUUUUCACGACG-----AUA
.........(((((.((....)).))))).(((((.((((......)))).......((((((((((.((((..........)))).))))))...)))).......)))))-----... ( -31.60)
>DroSim_CAF1 50533 115 + 1
AAAACGAAGGCGAAGGCGAAGGCGUUUGCGUGUCGAGCGACAUCAUUUGCAUAACAAUGCUGGAGAUAGAGACGAUUCAAAUUUUUGGUCUCCCAGAGCAAUUUUCACGACG-----AUA
.........(((((.((....)).))))).(((((.((((......)))).......((((((((((.((((..........)))).))))))...)))).......)))))-----... ( -31.60)
>DroEre_CAF1 58354 106 + 1
---------GCGAAGGCGAAGGCGUUUGCGUGUCGAGCGACAUCAUUUGCAUAACAAUGCUGGCGAUAGAGACGAUUCAAAUUUUUGGUCUCCCAGAGCAAUUUUCACGAUG-----AUA
---------(((((.((....)).)))))..(((....)))((((((.((((....))))..((....(((((.(..........).))))).....)).........))))-----)). ( -28.80)
>DroYak_CAF1 42579 115 + 1
AAAACGAAGGCGAAGGCGAAGGCGUUUGCGUGUCGAGCGACAUCAUUUGCAUAACAAUGCUGGAGAUAGAGACGAUUCAAAUUUUUGGUCUCCCAGAGCAAUUUUCACGACG-----AUA
.........(((((.((....)).))))).(((((.((((......)))).......((((((((((.((((..........)))).))))))...)))).......)))))-----... ( -31.60)
>consensus
AAAACGAAGGCGAAGGCGAAGGCGUUUGCGUGUCGAGCGACAUCAUUUGCAUAACAAUGCUGGAGAUAGAGACGAUUCAAAUUUUUGGUCUCCCAGAGCAAUUUUCACGACG_____AUA
.........(((((.((....)).)))))..((((.((((......)))).......((((((((((.((((..........)))).))))))...)))).......))))......... (-30.04 = -30.08 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:59 2006