Locus 6526

Sequence ID	2L_DroMel_CAF1
Location	18,367,424 – 18,367,714
Length	290
Max. P	0.926558

overview

Window 4

Location	18,367,424 – 18,367,532
Length	108
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	87.34
Mean single sequence MFE	-34.45
Consensus MFE	-26.26
Energy contribution	-28.15
Covariance contribution	1.89
Combinations/Pair	1.11
Mean z-score	-2.69
Structure conservation index	0.76
SVM decision value	0.24
SVM RNA-class probability	0.647890
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18367424 108 - 22407834
GUGGAUUUUCCAGGACUUUACUGACUUGCAUUUCUAUGCAGGA---CAGGACUCUUCUCAAAAGGGAAAUGGAGCCGUAAUAAAUGUCAGUUCUUCUUGGGGAAUACCCCA
(.(((((..((((((....((((((((((((....))))))).---..((.((((((((....))))...))))))..........)))))...))))))..))).)).). ( -37.40)
>DroSec_CAF1 211261 108 - 1
GUGGAUUUUCCAGGACUUUACUGACUUGCAUUUCUAUGCAGGA---CAGGACUCUUCUCAAAAGGGAAAUGGAGCCAUAAUAAAUGUCAGUUCUUCUUGGGGAAUACCCCA
(.(((((..((((((....((((((((((((....))))))).---..((.((((((((....))))...))))))..........)))))...))))))..))).)).). ( -37.40)
>DroSim_CAF1 220319 108 - 1
GUGGAUUUUCCAGGACUUUACUGACUUGCAUUUCUAUGCAGGA---CAGGACUCUUCUCAAAAGGGAAAUGGAGCCGUAAUAAAUGUCAGUUCUUCUUGGGGAAUACCCCA
(.(((((..((((((....((((((((((((....))))))).---..((.((((((((....))))...))))))..........)))))...))))))..))).)).). ( -37.40)
>DroEre_CAF1 211718 108 - 1
GUGGAUUUUCCACGACUUUACCGACUUGCAUUUCUAUGCAGGG---CAGGACUCUUUUCAAAAGGGAAAUGGAGCCGUAAUAAAUGUCAGUUCUUCUUAGGGAAUACCCCA
((((.....))))(((.((((...(((((((....))))))).---..((.((((((((......)))).)))))))))).....)))...........(((.....))). ( -31.20)
>DroYak_CAF1 221671 108 - 1
GUGGAUUUUCCAGGACUUUACCGACUUGCAUUUCUAUGCAGGG---CAGGACUCUUUUCAAGAGGGAAAUGGAGCCGUAAUAAAUGUCAGUUCUUCCUGGGGAAUACCCCA
(.(((((..((((((....((.(((((((((....))))))).---..((.((((((((......)))).))))))..........)).))...))))))..))).)).). ( -35.00)
>DroAna_CAF1 192572 102 - 1
GAGGAUUUUCCAGGAAUUUACUGACUUGCAUUUCUAUGCAGGAGGGCGUGCCUCCUGU----AGGAAUACGGUGCCAUAAUAAAUACCAGAUCCAGCUGGGACAUA-----
..(((((((((((((((.((......)).)))))).(((((((((.....))))))))----)))))...((((..........)))).)))))............----- ( -28.30)
>consensus
GUGGAUUUUCCAGGACUUUACUGACUUGCAUUUCUAUGCAGGA___CAGGACUCUUCUCAAAAGGGAAAUGGAGCCGUAAUAAAUGUCAGUUCUUCUUGGGGAAUACCCCA
..(((((((((((((....((((((((((((....)))))))......((.((((((((....))))...))))))..........)))))...))))))))))).))... (-26.26 = -28.15 +   1.89)

alignment

secondary structure

dotplot

Window 5

Location	18,367,498 – 18,367,612
Length	114
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	91.23
Mean single sequence MFE	-32.15
Consensus MFE	-27.88
Energy contribution	-27.63
Covariance contribution	-0.25
Combinations/Pair	1.13
Mean z-score	-1.48
Structure conservation index	0.87
SVM decision value	0.18
SVM RNA-class probability	0.620377
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18367498 114 + 22407834
GAAAUGCAAGUCAGUAAAGUCCUGGAAAAUCCACAAGGAUUUGCUCGGUGAUAGCUGAAAGCUUUCUCCCAUUCCCCACAUCGAGGUUUGGAUUUCCCUUUCGGGGAUUUUCCA
((((.((...(((((...(((((((.((((((....))))))..)))).))).)))))..))))))..(((..((.(.....).))..)))...((((.....))))....... ( -32.10)
>DroSec_CAF1 211335 114 + 1
GAAAUGCAAGUCAGUAAAGUCCUGGAAAAUCCACAAGGAUUUGCUCGGUGAUAGCUGAAAGCUUUCUCCCAUUCCCCACAUUGAGGUUUGGAUUUCCCUUUCGGGGAUUUUCCA
((((.((...(((((...(((((((.((((((....))))))..)))).))).)))))..))))))..(((..((.(.....).))..)))...((((.....))))....... ( -32.40)
>DroSim_CAF1 220393 114 + 1
GAAAUGCAAGUCAGUAAAGUCCUGGAAAAUCCACAAGGAUUUGCUCGGUGAUAGCUGAAAGCUUUUUCCCAUUCCCCACAUAGAGGUUUGGAUUUCCCUUUCGGGGAUUUUCCA
((((.((...(((((...(((((((.((((((....))))))..)))).))).)))))..))..))))(((..((.(.....).))..)))...((((.....))))....... ( -31.40)
>DroEre_CAF1 211792 114 + 1
GAAAUGCAAGUCGGUAAAGUCGUGGAAAAUCCACAAGGAUUUGCUCGGUGAUAGCUGAAAGCUUUUUCCCACUCCCUACAUCGAGAUUUGGAUUUCCCUUUCGGGGAUUUUCCA
.....(((((((((.....))((((.....))))...)))))))..((.((.(((.....)))...)))).(((........)))...((((..((((.....))))...)))) ( -31.40)
>DroYak_CAF1 221745 114 + 1
GAAAUGCAAGUCGGUAAAGUCCUGGAAAAUCCACAAGGAUUUGCUCGGUGAUAGCUGAAAGCUUUUUCCCAUUCCCCACAUAGAGGUUUGGAUUUCCCUUUCGGGGAUUUUCCA
((((.((...(((((...(((((((.((((((....))))))..)))).))).)))))..))..))))(((..((.(.....).))..)))...((((.....))))....... ( -30.70)
>DroAna_CAF1 192640 106 + 1
GAAAUGCAAGUCAGUAAAUUCCUGGAAAAUCCUCAAGGAUUUGCCUGGCGAUAGAUGAAAGCUUUCCC-------CUCCGCCGAGGG-CGGAUUUCCCUUUCGGGGAUUUUCCA
....(((......))).......(((((((((((((((((((((((((((..((..(((....)))..-------)).))))..)))-)))))...))))..))))))))))). ( -34.90)
>consensus
GAAAUGCAAGUCAGUAAAGUCCUGGAAAAUCCACAAGGAUUUGCUCGGUGAUAGCUGAAAGCUUUCUCCCAUUCCCCACAUCGAGGUUUGGAUUUCCCUUUCGGGGAUUUUCCA
((((.((...(((((...(((((((.((((((....))))))..)))).))).)))))..)))))).......................(((..((((.....))))...))). (-27.88 = -27.63 +  -0.25)

alignment

secondary structure

dotplot

Window 6

Location	18,367,572 – 18,367,678
Length	106
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	92.14
Mean single sequence MFE	-27.65
Consensus MFE	-23.27
Energy contribution	-23.42
Covariance contribution	0.14
Combinations/Pair	1.14
Mean z-score	-2.31
Structure conservation index	0.84
SVM decision value	1.06
SVM RNA-class probability	0.908025
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18367572 106 - 22407834
G-----AAACAAACAAUGUGCUAGUAUAUUGUUUGCAUAUUUCAUGACCUUUGACAACAAUCAACUACGAGUGGAAAAUCCCCGAAAGGGAAAUCCAAACCUCGAUGUGGG
(-----((((((((((((((....)))))))))))....))))....((.((((......))))...((((((((.....(((....)))...))))...))))....)). ( -28.10)
>DroSec_CAF1 211409 105 - 1
G-----AAACAAACAAUGUGCUGGUAUAU-GUUUGCAUAUUUCAUGACCUUUGACAACAAUCAACUACGAGUGGAAAAUCCCCGAAAGGGAAAUCCAAACCUCAAUGUGGG
.-----...((((((.((((....)))))-)))))((((((.........((((......))))....(((((((.....(((....)))...))))...))))))))).. ( -22.10)
>DroSim_CAF1 220467 106 - 1
G-----AAACAAACAAUGUGCUGGUAUAUUGUUUGCAUAUUUCAUGACCUUUGACAACAAUCAACUACGAGUGGAAAAUCCCCGAAAGGGAAAUCCAAACCUCUAUGUGGG
(-----((((((((((((((....)))))))))))....)))).......((((......))))(((((((((((.....(((....)))...))))...)))...)))). ( -26.30)
>DroEre_CAF1 211866 106 - 1
G-----AAACAAACAAUGUGCUGGUAUAUUGUUUGCAUAUUUCAUGACCUUUGACAACAAUCAACUACGAGUGGAAAAUCCCCGAAAGGGAAAUCCAAAUCUCGAUGUAGG
(-----((((((((((((((....)))))))))))....))))....(((((((......))))...((((((((.....(((....)))...))))...))))....))) ( -27.50)
>DroYak_CAF1 221819 106 - 1
G-----AAACAAACAAUGUGCUGGUAUAUUGUUUGCAUAUUUCAUGACCUUUGACAACAAUCAACUACGAGUGGAAAAUCCCCGAAAGGGAAAUCCAAACCUCUAUGUGGG
(-----((((((((((((((....)))))))))))....)))).......((((......))))(((((((((((.....(((....)))...))))...)))...)))). ( -26.30)
>DroAna_CAF1 192708 109 - 1
AAUGGCAAACAAACAAUGUGCCAGCGUAUUGUUUGCAUAUUUCAUGACCUUUGACAACAAUCAACCAGGAGUGGAAAAUCCCCGAAAGGGAAAUCCG-CCCUCGGCGGAG-
....((((((((...((((....)))).))))))))...((((((..(((((((......))))..))).))))))....(((....)))...((((-((...)))))).- ( -35.60)
>consensus
G_____AAACAAACAAUGUGCUGGUAUAUUGUUUGCAUAUUUCAUGACCUUUGACAACAAUCAACUACGAGUGGAAAAUCCCCGAAAGGGAAAUCCAAACCUCGAUGUGGG
.........(((((((((((....)))))))))))...............((((......))))(((((((((((.....(((....)))...))))...)))...)))). (-23.27 = -23.42 +   0.14)

alignment

secondary structure

dotplot

Window 7

Location	18,367,612 – 18,367,714
Length	102
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	95.00
Mean single sequence MFE	-22.76
Consensus MFE	-21.74
Energy contribution	-22.10
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.17
Structure conservation index	0.96
SVM decision value	1.18
SVM RNA-class probability	0.926558
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18367612 102 + 22407834
CUCGUAGUUGAUUGUUGUCAAAGGUCAUGAAAUAUGCAAACAAUAUACUAGCACAUUGUUUGUUU-----CCGAUCCGAUACGAUUAGCUAAUCGAAGCGAUAAACU-
.((((((((((((((.(((...((((..(((....(((((((((..........)))))))))))-----).)))).))))))))))))))..)))...........- ( -23.30)
>DroSec_CAF1 211449 101 + 1
CUCGUAGUUGAUUGUUGUCAAAGGUCAUGAAAUAUGCAAAC-AUAUACCAGCACAUUGUUUGUUU-----CCGAUCCGAUACGAUUAGCUAAUCGAAGCGAUAAACU-
.((((((((((((((.(((...((((..((((((.((((..-.............)))).)))))-----).)))).))))))))))))))..)))...........- ( -21.86)
>DroSim_CAF1 220507 102 + 1
CUCGUAGUUGAUUGUUGUCAAAGGUCAUGAAAUAUGCAAACAAUAUACCAGCACAUUGUUUGUUU-----CCGAUCCGAUACGAUUAGCUAAUCGAAGCGAUAAACU-
.((((((((((((((.(((...((((..(((....(((((((((..........)))))))))))-----).)))).))))))))))))))..)))...........- ( -23.30)
>DroEre_CAF1 211906 103 + 1
CUCGUAGUUGAUUGUUGUCAAAGGUCAUGAAAUAUGCAAACAAUAUACCAGCACAUUGUUUGUUU-----CCGAUCCGAUACGAUUAGCUAAUCGAAGCGAUAAACUC
.((((((((((((((.(((...((((..(((....(((((((((..........)))))))))))-----).)))).))))))))))))))..)))............ ( -23.30)
>DroYak_CAF1 221859 102 + 1
CUCGUAGUUGAUUGUUGUCAAAGGUCAUGAAAUAUGCAAACAAUAUACCAGCACAUUGUUUGUUU-----CCGAUCCGAUACGAUUAGCUAAUCGAAGCGAUAAACU-
.((((((((((((((.(((...((((..(((....(((((((((..........)))))))))))-----).)))).))))))))))))))..)))...........- ( -23.30)
>DroAna_CAF1 192746 107 + 1
CUCCUGGUUGAUUGUUGUCAAAGGUCAUGAAAUAUGCAAACAAUACGCUGGCACAUUGUUUGUUUGCCAUUCGAUCCGAUCCGAUUAGCUAAUCGAAGCGAUAAACU-
....((((((((((..(((...((((..(((....((((((((.(((.((...)).)))))))))))..))))))).))).))))))))))((((...)))).....- ( -21.50)
>consensus
CUCGUAGUUGAUUGUUGUCAAAGGUCAUGAAAUAUGCAAACAAUAUACCAGCACAUUGUUUGUUU_____CCGAUCCGAUACGAUUAGCUAAUCGAAGCGAUAAACU_
.((((((((((((((.(((...((((.........(((((((((..........))))))))).........)))).))))))))))))))..)))............ (-21.74 = -22.10 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:23 2006