Locus 3043

Sequence ID	X_DroMel_CAF1
Location	8,133,879 – 8,134,020
Length	141
Max. P	0.999195

overview

Window 8

Location	8,133,879 – 8,133,980
Length	101
Sequences	3
Columns	114
Reading direction	forward
Mean pairwise identity	75.38
Mean single sequence MFE	-26.63
Consensus MFE	-15.69
Energy contribution	-15.70
Covariance contribution	0.01
Combinations/Pair	1.14
Mean z-score	-1.71
Structure conservation index	0.59
SVM decision value	0.24
SVM RNA-class probability	0.650016
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8133879 101 + 22224390
AUGCCGAUUACCA-------AUCCGAAUCCGAUUUCGAUUCC------AAUUCAGAUUCCGAUUCCGUUCGCUUGGGCGGCAAUUUGGAGCCACAAAUCCAAAUUGAUUUAGAA
..((((....(((-------(..(((((..((((..((.((.------......)).)).))))..))))).)))).))))((((((((........))))))))......... ( -24.90)
>DroEre_CAF1 24129 94 + 1
AUUGCGAUUCCGA-------UUCCAAAGCAGAAUGCGAUUCCAAUUC------------AGAUUCCGCUCGCUUGGGCGGCAAU-UGGAGCCACAAAUCCAAAUUGAUUUAGAA
....(((((..((-------((.....((.....))(..(((((((.------------.....((((((....)))))).)))-))))..)...))))..)))))........ ( -20.50)
>DroYak_CAF1 24850 113 + 1
AUUCCGAUUCCGAUUCCCGAUUCCGAAUCAAAAUCCGAUUCCGAUUCCGAUCCAGAAUCGGAUUCCGCUCGCUUGGGCGGCAAU-UGGAGCCACAAAUCCAAAUUGAUUUAGAA
..((((((((.((((...((.((.(((((.......))))).)).)).))))..))))))))..((((((....))))))((((-((((........))).)))))........ ( -34.50)
>consensus
AUUCCGAUUCCGA_______UUCCGAAUCAGAAUCCGAUUCC_AUUC__AU_CAGA_UCAGAUUCCGCUCGCUUGGGCGGCAAU_UGGAGCCACAAAUCCAAAUUGAUUUAGAA
.....................((.(((((((..............................(((((((((....)))))).))).((((........))))..))))))).)). (-15.69 = -15.70 +   0.01)

alignment

secondary structure

dotplot

Window 9

Location	8,133,912 – 8,134,020
Length	108
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	77.01
Mean single sequence MFE	-31.58
Consensus MFE	-23.76
Energy contribution	-24.20
Covariance contribution	0.44
Combinations/Pair	1.14
Mean z-score	-2.72
Structure conservation index	0.75
SVM decision value	3.43
SVM RNA-class probability	0.999195
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8133912 108 + 22224390
CC------AAUUCAGAUUCCGAUUCCGUUCGCUUGGGCGGCAAUUUGGAGCCACAAAUCCA------AAUUGAUUUAGAAUGCCUAAGCGGGCAUCACAAGCAAAUAAUAAGCCGAGGCA
..------..................(((((((((((((.(((((((((........))))------)))))........)))))))))))))..................((....)). ( -34.40)
>DroEre_CAF1 24162 101 + 1
CCAAUUC------------AGAUUCCGCUCGCUUGGGCGGCAAU-UGGAGCCACAAAUCCA------AAUUGAUUUAGAAUGCCUAAGCGGGCAUCACAAGCAAAUAAUAAGCCGGGGCA
.......------------.(.(((((((((((((((((((...-....)))..(((((..------....))))).....)))))))))))).......((.........)).))))). ( -33.00)
>DroYak_CAF1 24890 113 + 1
CCGAUUCCGAUCCAGAAUCGGAUUCCGCUCGCUUGGGCGGCAAU-UGGAGCCACAAAUCCA------AAUUGAUUUAGAAUGCCUAAGCGGGCAUCACAAGCAAAUAAUAAGCCGGGGCA
(((((((.......))))))).....(((((((((((((((...-....)))..(((((..------....))))).....))))))))))))..................((....)). ( -41.50)
>DroAna_CAF1 34523 103 + 1
----------------AAAGCAUUCCGCUCGCUUGGCUGAUCAU-UCAAGCCACAAAUCCAAAGCAAAAUUGAUUUAAAAGGCCUAAACGGGCAUCACAACCAAAUAAUAAGCAAAGUCA
----------------..(((.....))).((((((((((....-)).)))).............................((((....))))................))))....... ( -17.40)
>consensus
CC______________AUCGGAUUCCGCUCGCUUGGGCGGCAAU_UGGAGCCACAAAUCCA______AAUUGAUUUAGAAUGCCUAAGCGGGCAUCACAAGCAAAUAAUAAGCCGAGGCA
..........................(((((((((((((((........)))..(((((............))))).....))))))))))))..................((....)). (-23.76 = -24.20 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	8,133,912 – 8,134,020
Length	108
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	77.01
Mean single sequence MFE	-32.35
Consensus MFE	-19.42
Energy contribution	-20.55
Covariance contribution	1.13
Combinations/Pair	1.08
Mean z-score	-1.69
Structure conservation index	0.60
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8133912 108 - 22224390
UGCCUCGGCUUAUUAUUUGCUUGUGAUGCCCGCUUAGGCAUUCUAAAUCAAUU------UGGAUUUGUGGCUCCAAAUUGCCGCCCAAGCGAACGGAAUCGGAAUCUGAAUU------GG
(((((.(((.((((((......))))))...))).)))))........(((((------..((((((((((........))))).....(((......))))))))..))))------). ( -33.20)
>DroEre_CAF1 24162 101 - 1
UGCCCCGGCUUAUUAUUUGCUUGUGAUGCCCGCUUAGGCAUUCUAAAUCAAUU------UGGAUUUGUGGCUCCA-AUUGCCGCCCAAGCGAGCGGAAUCU------------GAAUUGG
....((((.(((...(((((((((((((((......))))))..........(------(((....(((((....-...))))))))))))))))))...)------------)).)))) ( -29.00)
>DroYak_CAF1 24890 113 - 1
UGCCCCGGCUUAUUAUUUGCUUGUGAUGCCCGCUUAGGCAUUCUAAAUCAAUU------UGGAUUUGUGGCUCCA-AUUGCCGCCCAAGCGAGCGGAAUCCGAUUCUGGAUCGGAAUCGG
.((....))......(((((((((((((((......))))))..........(------(((....(((((....-...))))))))))))))))))..(((((((((...))))))))) ( -39.20)
>DroAna_CAF1 34523 103 - 1
UGACUUUGCUUAUUAUUUGGUUGUGAUGCCCGUUUAGGCCUUUUAAAUCAAUUUUGCUUUGGAUUUGUGGCUUGA-AUGAUCAGCCAAGCGAGCGGAAUGCUUU----------------
....(((((((....((((((((.......((((((((((...((((((............)))))).)))))))-)))..)))))))).))))))).......---------------- ( -28.00)
>consensus
UGCCCCGGCUUAUUAUUUGCUUGUGAUGCCCGCUUAGGCAUUCUAAAUCAAUU______UGGAUUUGUGGCUCCA_AUUGCCGCCCAAGCGAGCGGAAUCCGAU______________GG
.((....))......(((((((((((((((......)))))).................(((....(((((........)))))))).)))))))))....................... (-19.42 = -20.55 +   1.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:37 2006