Locus 1924

Sequence ID	2L_DroMel_CAF1
Location	5,230,674 – 5,230,861
Length	187
Max. P	0.998790

overview

Window 7

Location	5,230,674 – 5,230,790
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.81
Mean single sequence MFE	-40.96
Consensus MFE	-30.89
Energy contribution	-32.04
Covariance contribution	1.15
Combinations/Pair	1.00
Mean z-score	-5.13
Structure conservation index	0.75
SVM decision value	3.18
SVM RNA-class probability	0.998663
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5230674 116 + 22407834
AAAA-AGUUCGAAAAGCAAUUCCAAACCGAUCAA--CCCAGCAACAUGUUGUUGCUGCUGCUACCGAAGCAUUUGCUACUGCAGCAGCAACAUGUUGCUUCUAGCCGU-UUGAUUUUGGC
..((-(((.((((..((...((......))....--...(((((((((((((((((((((((.....)))).........)))))))))))))))))))....))..)-))))))))... ( -39.20)
>DroSec_CAF1 8026 103 + 1
AAAA-AGGUCGAAAAGCAAUUCCAAACCGAUCCGUCGCCAGCAACAUGUUGUUGC---------------AAUUGCUACUGCAGCAGCAACAUGUUGCUACUCGCCGU-UUGCUUUUGGC
....-..(((.((((((((........(((....)))..((((((((((((((((---------------...(((....))))))))))))))))))).........-))))))))))) ( -38.20)
>DroSim_CAF1 8946 103 + 1
AAAA-AGUUCGAAAAGCAAUUCCAAACCGAACC---GCCAGCAACAUGUUGUUGC------------AGCAAUUGCUACUGCAGCAGCAACAUGUUGCUACUCGCCGU-UUGCUUUUGGC
....-................(((((.(((((.---((.((((((((((((((((------------.(((........))).))))))))))))))))....)).))-)))..))))). ( -38.60)
>DroEre_CAF1 822 117 + 1
AAAAGAGAUCCAAAAGCAAUUCCAAAACGAACC---GCCAGCAACAUGUUGUUGCUGCUACAAGCGAAGCAAUUGCUACUGCAGCAGCAACAUGUUGCUCCUCGCCUUUUUGCUUUGGGC
........((((((.(((((((......)))..---((.(((((((((((((((((((....(((((.....)))))...)))))))))))))))))))....))....)))))))))). ( -46.60)
>DroYak_CAF1 9826 115 + 1
AAAA-AGAUCCAAAAGCAAUUCCAAAUCGAUUC---ACCAGCAACAUGUUGUUGCCGCUACUACCGAAGCAAUUGCUACUGCAGCAGCAACAUGUUGCUCCUUGCCGU-UUGCUUUUGGC
....-....((((((((((...(((...(....---..)((((((((((((((((.(((........)))...(((....)))))))))))))))))))..)))....-)))))))))). ( -42.20)
>consensus
AAAA_AGAUCGAAAAGCAAUUCCAAACCGAUCC___GCCAGCAACAUGUUGUUGC_GCU_C_A_CGAAGCAAUUGCUACUGCAGCAGCAACAUGUUGCUACUCGCCGU_UUGCUUUUGGC
.........(.((((((((.((......)).........((((((((((((((((.(((........)))...(((....)))))))))))))))))))..........)))))))).). (-30.89 = -32.04 +   1.15)

alignment

secondary structure

dotplot

Window 8

Location	5,230,674 – 5,230,790
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.81
Mean single sequence MFE	-43.84
Consensus MFE	-27.19
Energy contribution	-28.71
Covariance contribution	1.52
Combinations/Pair	1.03
Mean z-score	-4.34
Structure conservation index	0.62
SVM decision value	2.60
SVM RNA-class probability	0.995678
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5230674 116 - 22407834
GCCAAAAUCAA-ACGGCUAGAAGCAACAUGUUGCUGCUGCAGUAGCAAAUGCUUCGGUAGCAGCAGCAACAACAUGUUGCUGGG--UUGAUCGGUUUGGAAUUGCUUUUCGAACU-UUUU
...........-.(((((...(((((((((((((((((((.(.(((....))).)....)))))))))...)))))))))).))--)))...(((((((((.....)))))))))-.... ( -46.30)
>DroSec_CAF1 8026 103 - 1
GCCAAAAGCAA-ACGGCGAGUAGCAACAUGUUGCUGCUGCAGUAGCAAUU---------------GCAACAACAUGUUGCUGGCGACGGAUCGGUUUGGAAUUGCUUUUCGACCU-UUUU
.(.((((((((-.((.((..(((((((((((((.((((((....)))...---------------))).))))))))))))).)).))..((......)).)))))))).)....-.... ( -35.50)
>DroSim_CAF1 8946 103 - 1
GCCAAAAGCAA-ACGGCGAGUAGCAACAUGUUGCUGCUGCAGUAGCAAUUGCU------------GCAACAACAUGUUGCUGGC---GGUUCGGUUUGGAAUUGCUUUUCGAACU-UUUU
(((....((..-...))....((((((((((((.(((.(((((....))))).------------))).)))))))))))))))---.....(((((((((.....)))))))))-.... ( -41.60)
>DroEre_CAF1 822 117 - 1
GCCCAAAGCAAAAAGGCGAGGAGCAACAUGUUGCUGCUGCAGUAGCAAUUGCUUCGCUUGUAGCAGCAACAACAUGUUGCUGGC---GGUUCGUUUUGGAAUUGCUUUUGGAUCUCUUUU
(((...........)))(((((((((((((((((((((((((((((....)))..)).))))))))))...))))))))))(((---(((((......))))))))......)))).... ( -48.50)
>DroYak_CAF1 9826 115 - 1
GCCAAAAGCAA-ACGGCAAGGAGCAACAUGUUGCUGCUGCAGUAGCAAUUGCUUCGGUAGUAGCGGCAACAACAUGUUGCUGGU---GAAUCGAUUUGGAAUUGCUUUUGGAUCU-UUUU
.((((((((((-....((...(((((((((((((((((((...(((....)))...))))))))(....))))))))))))..)---)..((......)).))))))))))....-.... ( -47.30)
>consensus
GCCAAAAGCAA_ACGGCGAGGAGCAACAUGUUGCUGCUGCAGUAGCAAUUGCUUCG_U_G_AGC_GCAACAACAUGUUGCUGGC___GGAUCGGUUUGGAAUUGCUUUUCGAACU_UUUU
.(.((((((((..........((((((((((((.((((((......................)))))).)))))))))))).........((......)).)))))))).)......... (-27.19 = -28.71 +   1.52)

alignment

secondary structure

dotplot

Window 9

Location	5,230,711 – 5,230,830
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.92
Mean single sequence MFE	-45.06
Consensus MFE	-37.76
Energy contribution	-39.11
Covariance contribution	1.35
Combinations/Pair	1.00
Mean z-score	-5.63
Structure conservation index	0.84
SVM decision value	3.23
SVM RNA-class probability	0.998790
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5230711 119 + 22407834
GCAACAUGUUGUUGCUGCUGCUACCGAAGCAUUUGCUACUGCAGCAGCAACAUGUUGCUUCUAGCCGU-UUGAUUUUGGCCAGACUGUUUGACUGCUGGCCAUUAUUGUUACGCUUUUUU
((((((((((((((((((((((.....)))).........))))))))))))))))))....(((.((-.((((..(((((((...(.....)..)))))))..))))..)))))..... ( -50.50)
>DroSec_CAF1 8065 104 + 1
GCAACAUGUUGUUGC---------------AAUUGCUACUGCAGCAGCAACAUGUUGCUACUCGCCGU-UUGCUUUUGGCCAAACUGUUUGACUGCUGGCCAUUAUUGUUACGCUUUUUU
(((((((((((((((---------------...(((....)))))))))))))))))).....((.((-..((...((((((....((......)))))))).....)).))))...... ( -38.00)
>DroSim_CAF1 8982 107 + 1
GCAACAUGUUGUUGC------------AGCAAUUGCUACUGCAGCAGCAACAUGUUGCUACUCGCCGU-UUGCUUUUGGCCAGACUGUUUGACUGCUGGCCAUUAUUGUUACGCUUUUUU
(((((((((((((((------------.(((........))).))))))))))))))).....((.((-..((...(((((((...(.....)..))))))).....)).))))...... ( -43.20)
>DroEre_CAF1 859 120 + 1
GCAACAUGUUGUUGCUGCUACAAGCGAAGCAAUUGCUACUGCAGCAGCAACAUGUUGCUCCUCGCCUUUUUGCUUUGGGCCAGACUGUUUGACUGCUGGCCAUUAUUGUUACGCUUUUUU
((((((((((((((((((....(((((.....)))))...)))))))))))))))))).....((............((((((...(.....)..))))))...........))...... ( -48.80)
>DroYak_CAF1 9862 119 + 1
GCAACAUGUUGUUGCCGCUACUACCGAAGCAAUUGCUACUGCAGCAGCAACAUGUUGCUCCUUGCCGU-UUGCUUUUGGCCAGACUGUUUGACUGCUGGCCAUUAUUGUUACGCUUUUUU
(((((((((((((((.(((........)))...(((....)))))))))))))))))).....((.((-..((...(((((((...(.....)..))))))).....)).))))...... ( -44.80)
>consensus
GCAACAUGUUGUUGC_GCU_C_A_CGAAGCAAUUGCUACUGCAGCAGCAACAUGUUGCUACUCGCCGU_UUGCUUUUGGCCAGACUGUUUGACUGCUGGCCAUUAUUGUUACGCUUUUUU
(((((((((((((((.(((........)))...(((....)))))))))))))))))).....((.((........(((((((...(.....)..)))))))........))))...... (-37.76 = -39.11 +   1.35)

alignment

secondary structure

dotplot

Window 0

Location	5,230,711 – 5,230,830
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.92
Mean single sequence MFE	-40.45
Consensus MFE	-31.80
Energy contribution	-33.16
Covariance contribution	1.36
Combinations/Pair	1.07
Mean z-score	-4.85
Structure conservation index	0.79
SVM decision value	3.20
SVM RNA-class probability	0.998722
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5230711 119 - 22407834
AAAAAAGCGUAACAAUAAUGGCCAGCAGUCAAACAGUCUGGCCAAAAUCAA-ACGGCUAGAAGCAACAUGUUGCUGCUGCAGUAGCAAAUGCUUCGGUAGCAGCAGCAACAACAUGUUGC
.....(((..........((((((((.(.....).).))))))).......-...)))....((((((((((((((((((.(.(((....))).)....)))))))))...))))))))) ( -44.35)
>DroSec_CAF1 8065 104 - 1
AAAAAAGCGUAACAAUAAUGGCCAGCAGUCAAACAGUUUGGCCAAAAGCAA-ACGGCGAGUAGCAACAUGUUGCUGCUGCAGUAGCAAUU---------------GCAACAACAUGUUGC
......((..........((((((((.(.....).).)))))))...((..-...))..)).(((((((((((.((((((....)))...---------------))).))))))))))) ( -32.10)
>DroSim_CAF1 8982 107 - 1
AAAAAAGCGUAACAAUAAUGGCCAGCAGUCAAACAGUCUGGCCAAAAGCAA-ACGGCGAGUAGCAACAUGUUGCUGCUGCAGUAGCAAUUGCU------------GCAACAACAUGUUGC
......((..........((((((((.(.....).).)))))))...((..-...))..)).(((((((((((.(((.(((((....))))).------------))).))))))))))) ( -38.80)
>DroEre_CAF1 859 120 - 1
AAAAAAGCGUAACAAUAAUGGCCAGCAGUCAAACAGUCUGGCCCAAAGCAAAAAGGCGAGGAGCAACAUGUUGCUGCUGCAGUAGCAAUUGCUUCGCUUGUAGCAGCAACAACAUGUUGC
...................(((((((.(.....).).))))))....((......)).....((((((((((((((((((((((((....)))..)).))))))))))...))))))))) ( -42.70)
>DroYak_CAF1 9862 119 - 1
AAAAAAGCGUAACAAUAAUGGCCAGCAGUCAAACAGUCUGGCCAAAAGCAA-ACGGCAAGGAGCAACAUGUUGCUGCUGCAGUAGCAAUUGCUUCGGUAGUAGCGGCAACAACAUGUUGC
..................((((((((.(.....).).)))))))...((..-...)).....((((((((((((((((((...(((....)))...))))))))(....))))))))))) ( -44.30)
>consensus
AAAAAAGCGUAACAAUAAUGGCCAGCAGUCAAACAGUCUGGCCAAAAGCAA_ACGGCGAGGAGCAACAUGUUGCUGCUGCAGUAGCAAUUGCUUCG_U_G_AGC_GCAACAACAUGUUGC
.......(((........((((((((.(.....).).)))))))........))).......(((((((((((.((((((......................)))))).))))))))))) (-31.80 = -33.16 +   1.36)

alignment

secondary structure

dotplot

Window 1

Location	5,230,751 – 5,230,861
Length	110
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.53
Mean single sequence MFE	-36.63
Consensus MFE	-29.34
Energy contribution	-29.62
Covariance contribution	0.28
Combinations/Pair	1.04
Mean z-score	-1.91
Structure conservation index	0.80
SVM decision value	0.99
SVM RNA-class probability	0.895888
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5230751 110 + 22407834
GCAGCAGCAACAUGUUGCUUCUAGCCGU-UUGAUUUUGGCCAGACUGUUUGACUGCUGGCCAUUAUUGUUACGCUUUUUUGGUCACCUGAUGAUGAAUCAAACAUUGGCGA---------
((((((......)))))).....(((((-(((((..(((((((...(.....)..)))))))((((..(((.(((.....)))....)))..)))))))))))...)))..--------- ( -34.20)
>DroSec_CAF1 8090 119 + 1
GCAGCAGCAACAUGUUGCUACUCGCCGU-UUGCUUUUGGCCAAACUGUUUGACUGCUGGCCAUUAUUGUUACGCUUUUUUGGUCACCUGAUGAUGAAUCAAACAUUGGCGAACGGCCACC
((((((......)))))).....(((((-(((((..((((((((..((.((((..............)))).))...))))))))..((((.....))))......)))))))))).... ( -37.74)
>DroSim_CAF1 9010 119 + 1
GCAGCAGCAACAUGUUGCUACUCGCCGU-UUGCUUUUGGCCAGACUGUUUGACUGCUGGCCAUUAUUGUUACGCUUUUUUGGUCACCUGAUGAUGAAUCAAACAUUGGCGAACGGCCACC
((((((......)))))).....(((((-(((((..(((((((...(.....)..)))))))((((..(((.(((.....)))....)))..))))..........)))))))))).... ( -40.60)
>DroEre_CAF1 899 119 + 1
GCAGCAGCAACAUGUUGCUCCUCGCCUUUUUGCUUUGGGCCAGACUGUUUGACUGCUGGCCAUUAUUGUUACGCUUUUUUGGUCACCUGAUGAUGAAUCAAACAUUGGCGACCGGCCAC-
((((((......)))))).....(((...........((((((...(.....)..))))))...................((((.((.((((.(......).)))))).)))))))...- ( -34.30)
>DroYak_CAF1 9902 118 + 1
GCAGCAGCAACAUGUUGCUCCUUGCCGU-UUGCUUUUGGCCAGACUGUUUGACUGCUGGCCAUUAUUGUUACGCUUUUUUGGUCACCUGAUGAUGAAUCAAACAUUGGCGACCGGCCAC-
((((((......)))))).....(((((-..((...(((((((...(.....)..))))))).....)).))........((((.((.((((.(......).)))))).)))))))...- ( -36.30)
>consensus
GCAGCAGCAACAUGUUGCUACUCGCCGU_UUGCUUUUGGCCAGACUGUUUGACUGCUGGCCAUUAUUGUUACGCUUUUUUGGUCACCUGAUGAUGAAUCAAACAUUGGCGAACGGCCAC_
((((((......))))))...(((((...........((((((...(.....)..)))))).((((..(((.(((.....)))....)))..))))..........)))))......... (-29.34 = -29.62 +   0.28)

alignment

secondary structure

dotplot

Window 2

Location	5,230,751 – 5,230,861
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.53
Mean single sequence MFE	-37.46
Consensus MFE	-29.86
Energy contribution	-31.30
Covariance contribution	1.44
Combinations/Pair	1.03
Mean z-score	-2.65
Structure conservation index	0.80
SVM decision value	2.04
SVM RNA-class probability	0.986465
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5230751 110 - 22407834
---------UCGCCAAUGUUUGAUUCAUCAUCAGGUGACCAAAAAAGCGUAACAAUAAUGGCCAGCAGUCAAACAGUCUGGCCAAAAUCAA-ACGGCUAGAAGCAACAUGUUGCUGCUGC
---------..(((...((((((((((((....)))))....................((((((((.(.....).).)))))))..)))))-)))))(((.(((((....))))).))). ( -31.60)
>DroSec_CAF1 8090 119 - 1
GGUGGCCGUUCGCCAAUGUUUGAUUCAUCAUCAGGUGACCAAAAAAGCGUAACAAUAAUGGCCAGCAGUCAAACAGUUUGGCCAAAAGCAA-ACGGCGAGUAGCAACAUGUUGCUGCUGC
....((((((.((..((((((...(((((....)))))......))))))........((((((((.(.....).).)))))))...)).)-))))).((((((((....)))))))).. ( -38.90)
>DroSim_CAF1 9010 119 - 1
GGUGGCCGUUCGCCAAUGUUUGAUUCAUCAUCAGGUGACCAAAAAAGCGUAACAAUAAUGGCCAGCAGUCAAACAGUCUGGCCAAAAGCAA-ACGGCGAGUAGCAACAUGUUGCUGCUGC
....((((((.((..((((((...(((((....)))))......))))))........((((((((.(.....).).)))))))...)).)-))))).((((((((....)))))))).. ( -41.30)
>DroEre_CAF1 899 119 - 1
-GUGGCCGGUCGCCAAUGUUUGAUUCAUCAUCAGGUGACCAAAAAAGCGUAACAAUAAUGGCCAGCAGUCAAACAGUCUGGCCCAAAGCAAAAAGGCGAGGAGCAACAUGUUGCUGCUGC
-.((((((((((((..((..(((....))).)))))))))......(.....)......)))))(((((.......(((.(((...........))).)))(((((....)))))))))) ( -36.90)
>DroYak_CAF1 9902 118 - 1
-GUGGCCGGUCGCCAAUGUUUGAUUCAUCAUCAGGUGACCAAAAAAGCGUAACAAUAAUGGCCAGCAGUCAAACAGUCUGGCCAAAAGCAA-ACGGCAAGGAGCAACAUGUUGCUGCUGC
-...((((((((((..((..(((....))).)))))))))..................((((((((.(.....).).))))))).......-..))).((.(((((....))))).)).. ( -38.60)
>consensus
_GUGGCCGGUCGCCAAUGUUUGAUUCAUCAUCAGGUGACCAAAAAAGCGUAACAAUAAUGGCCAGCAGUCAAACAGUCUGGCCAAAAGCAA_ACGGCGAGGAGCAACAUGUUGCUGCUGC
.(((((...(((((.((((((...(((((....)))))......))))))........((((((((.(.....).).)))))))..........)))))..(((((....)))))))))) (-29.86 = -31.30 +   1.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:03 2006