Locus 7333

Sequence ID	2L_DroMel_CAF1
Location	20,477,396 – 20,477,594
Length	198
Max. P	0.999516

overview

Window 2

Location	20,477,396 – 20,477,516
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.54
Mean single sequence MFE	-47.32
Consensus MFE	-38.72
Energy contribution	-39.80
Covariance contribution	1.08
Combinations/Pair	1.09
Mean z-score	-1.84
Structure conservation index	0.82
SVM decision value	1.15
SVM RNA-class probability	0.922403
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20477396 120 + 22407834
CGGGCGGGGGUCCCUGGGAACGGCGGCCACACAGCAGUGUACUCUGUGUACUUGGCUCAUGCAUAACGCAAAUGCUGGAAACGCCGCAAGGAGCCGCAUCGGCAUCCUUGCCAGUUUCGU
....((((....))))(((((((((.((((((((.((....))))))))....(((...(((.....)))...)))))...))))(((((((((((...)))).)))))))..))))).. ( -52.00)
>DroSec_CAF1 30403 120 + 1
CGGGCGGGGGUCCCUGGCAACGGCGGCCACACAGCAGUGUACUCUGUGUACUUUGCUCAUGCAUAACGCAAAUGCUGGAAACGCCGCAAGGAGCCACAUCGGCAUCCUUGCCAGUUUCGU
.(((((((((((.(((....))).))))((((((.((....))))))))..)))))))..((((.......))))..(((((...((((((((((.....))).)))))))..))))).. ( -51.10)
>DroSim_CAF1 34180 120 + 1
CGGGCGGGGGUCCCUGGAAGCGGCGGCCACACAGCAGUGUACUCUGUGUACUUGGCUCAUGCAUAACGCAAAUGCUGGAAACGCCGCAAGGAGCCACAUCGGCAUCCUUGCCAGUUUCGU
....((((....))))(((((((((.((((((((.((....))))))))....(((...(((.....)))...)))))...))))((((((((((.....))).)))))))..))))).. ( -51.70)
>DroEre_CAF1 32497 114 + 1
CGGGCGGGGGUCCAUUGAAAUGGCGGCCACGCAGCA-AGUACAC-----ACUUGGCCCAUUCAUAACGCAAAUGCUGGAGACGCCGCAAGGAGCCGCAGCGGCAUCCUUGCCAGUUUCGU
.((((....))))...(((((((((.(((.(((.((-(((....-----)))))((...........))...))))))...))))(((((((((((...)))).)))))))..))))).. ( -43.90)
>DroYak_CAF1 29594 115 + 1
CGGGCGGGGGUCCAUUGAAAUAGCGGCCACACAACAGAGUACAC-----ACUUGGCUCAUGCAUAACGCAAAUGCUGGAAACGCCGCAAGGAGCCACAUCGGCAUCCUUGCCAGUUUCGU
.((((....))))...(((((.(((.(((((.....((((.((.-----...)))))).(((.....)))..)).)))...))).((((((((((.....))).)))))))..))))).. ( -37.90)
>consensus
CGGGCGGGGGUCCCUGGAAACGGCGGCCACACAGCAGUGUACUCUGUGUACUUGGCUCAUGCAUAACGCAAAUGCUGGAAACGCCGCAAGGAGCCACAUCGGCAUCCUUGCCAGUUUCGU
.((((....))))...(((((((((......(((((..((((.....))))........(((.....)))..)))))....))))((((((((((.....))).)))))))..))))).. (-38.72 = -39.80 +   1.08)

alignment

secondary structure

dotplot

Window 3

Location	20,477,436 – 20,477,554
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.05
Mean single sequence MFE	-39.80
Consensus MFE	-36.98
Energy contribution	-36.86
Covariance contribution	-0.12
Combinations/Pair	1.06
Mean z-score	-2.23
Structure conservation index	0.93
SVM decision value	3.68
SVM RNA-class probability	0.999516
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20477436 118 + 22407834
ACUCUGUGUACUUGGCUCAUGCAUAACGCAAAUGCUGGAAACGCCGCAAGGAGCCGCAUCGGCAUCCUUGCCAGUUUCGUCCUCGUCGAGGUCCCAGCAUGUCCAC--GCAAUAACGAUU
....(((((....(((...(((.....))).(((((((((((...(((((((((((...)))).)))))))..)))))(.((((...)))).).))))))))).))--)))......... ( -42.20)
>DroSec_CAF1 30443 120 + 1
ACUCUGUGUACUUUGCUCAUGCAUAACGCAAAUGCUGGAAACGCCGCAAGGAGCCACAUCGGCAUCCUUGCCAGUUUCGUCCUCGUGGAGGUCCCAGCAUGUCCAUGUGCAAUAACGAUU
......(((...((((.(((((.....))..(((((((((((...((((((((((.....))).)))))))..)))))(.((((...)))).).))))))....))).))))..)))... ( -42.10)
>DroSim_CAF1 34220 118 + 1
ACUCUGUGUACUUGGCUCAUGCAUAACGCAAAUGCUGGAAACGCCGCAAGGAGCCACAUCGGCAUCCUUGCCAGUUUCGUCCUCGUGGAGGUCCCAGCAUGUCCAC--GCAAUAACGAUU
....(((((....(((...(((.....))).(((((((((((...((((((((((.....))).)))))))..)))))(.((((...)))).).))))))))).))--)))......... ( -41.40)
>DroEre_CAF1 32536 112 + 1
ACAC-----ACUUGGCCCAUUCAUAACGCAAAUGCUGGAGACGCCGCAAGGAGCCGCAGCGGCAUCCUUGCCAGUUUCGUCCUC-CGGAGGUCCCAGCAUGACCAC--GCAAUAACGAUU
....-----..................((..(((((((.(((...(((((((((((...)))).)))))))...(((((.....-)))))))))))))))......--)).......... ( -35.50)
>DroYak_CAF1 29634 113 + 1
ACAC-----ACUUGGCUCAUGCAUAACGCAAAUGCUGGAAACGCCGCAAGGAGCCACAUCGGCAUCCUUGCCAGUUUCGUCCUCGUGGAGGUCCCAGCGUGUCCAC--GCAAUAACGAUU
....-----.....((...(((.....))).(((((((((((...((((((((((.....))).)))))))..)))))(.((((...)))).).))))))......--)).......... ( -37.80)
>consensus
ACUCUGUGUACUUGGCUCAUGCAUAACGCAAAUGCUGGAAACGCCGCAAGGAGCCACAUCGGCAUCCUUGCCAGUUUCGUCCUCGUGGAGGUCCCAGCAUGUCCAC__GCAAUAACGAUU
..............((...(((.....))).(((((((((((...((((((((((.....))).)))))))..)))))(.((((...)))).).))))))........)).......... (-36.98 = -36.86 +  -0.12)

alignment

secondary structure

dotplot

Window 4

Location	20,477,436 – 20,477,554
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.05
Mean single sequence MFE	-41.94
Consensus MFE	-36.18
Energy contribution	-35.98
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-1.28
Structure conservation index	0.86
SVM decision value	0.22
SVM RNA-class probability	0.640976
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20477436 118 - 22407834
AAUCGUUAUUGC--GUGGACAUGCUGGGACCUCGACGAGGACGAAACUGGCAAGGAUGCCGAUGCGGCUCCUUGCGGCGUUUCCAGCAUUUGCGUUAUGCAUGAGCCAAGUACACAGAGU
..(((((((.((--(..((..(((((...((((...))))..((((((.(((((((.((((...))))))))))).).))))))))))))..))).))).))))................ ( -43.10)
>DroSec_CAF1 30443 120 - 1
AAUCGUUAUUGCACAUGGACAUGCUGGGACCUCCACGAGGACGAAACUGGCAAGGAUGCCGAUGUGGCUCCUUGCGGCGUUUCCAGCAUUUGCGUUAUGCAUGAGCAAAGUACACAGAGU
....(((..((((.(((.(.((((((...((((...))))..((((((.(((((((.(((.....)))))))))).).))))))))))).).)))..))))..))).............. ( -41.40)
>DroSim_CAF1 34220 118 - 1
AAUCGUUAUUGC--GUGGACAUGCUGGGACCUCCACGAGGACGAAACUGGCAAGGAUGCCGAUGUGGCUCCUUGCGGCGUUUCCAGCAUUUGCGUUAUGCAUGAGCCAAGUACACAGAGU
..(((((((.((--(..((..(((((...((((...))))..((((((.(((((((.(((.....)))))))))).).))))))))))))..))).))).))))................ ( -41.90)
>DroEre_CAF1 32536 112 - 1
AAUCGUUAUUGC--GUGGUCAUGCUGGGACCUCCG-GAGGACGAAACUGGCAAGGAUGCCGCUGCGGCUCCUUGCGGCGUCUCCAGCAUUUGCGUUAUGAAUGGGCCAAGU-----GUGU
..(((((...((--(..(..((((((((((..((.-.((.......)).(((((((.((((...))))))))))))).))).))))))))..)))....))))).......-----.... ( -42.00)
>DroYak_CAF1 29634 113 - 1
AAUCGUUAUUGC--GUGGACACGCUGGGACCUCCACGAGGACGAAACUGGCAAGGAUGCCGAUGUGGCUCCUUGCGGCGUUUCCAGCAUUUGCGUUAUGCAUGAGCCAAGU-----GUGU
...(((...(((--.((((.(((((....((((...)))).........(((((((.(((.....))))))))))))))).)))))))...)))..((((((.......))-----)))) ( -41.30)
>consensus
AAUCGUUAUUGC__GUGGACAUGCUGGGACCUCCACGAGGACGAAACUGGCAAGGAUGCCGAUGUGGCUCCUUGCGGCGUUUCCAGCAUUUGCGUUAUGCAUGAGCCAAGUACACAGAGU
...(((...(((...((((.(((((....((((...)))).........(((((((.((((...)))))))))))))))).)))))))...))).......................... (-36.18 = -35.98 +  -0.20)

alignment

secondary structure

dotplot

Window 5

Location	20,477,476 – 20,477,594
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.79
Mean single sequence MFE	-37.85
Consensus MFE	-35.04
Energy contribution	-35.08
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.98
Structure conservation index	0.93
SVM decision value	2.87
SVM RNA-class probability	0.997477
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20477476 118 + 22407834
ACGCCGCAAGGAGCCGCAUCGGCAUCCUUGCCAGUUUCGUCCUCGUCGAGGUCCCAGCAUGUCCAC--GCAAUAACGAUUGCGGGCAUAAUGCCCAUAAUGUCCUCAUAAUUACUGCCCA
.....(((((((((((...)))).)))))))((((..((....))..((((.....((((......--(((((....)))))((((.....))))...))))))))......)))).... ( -37.90)
>DroSec_CAF1 30483 120 + 1
ACGCCGCAAGGAGCCACAUCGGCAUCCUUGCCAGUUUCGUCCUCGUGGAGGUCCCAGCAUGUCCAUGUGCAAUAACGAUUGCGGGCAUAAUGCCCAUAAUGUCCUCAUAAUUACUGCCCA
.....((((((((((.....))).)))))))((((........((((((.((......)).)))))).(((((....)))))((((.....)))).................)))).... ( -38.30)
>DroSim_CAF1 34260 118 + 1
ACGCCGCAAGGAGCCACAUCGGCAUCCUUGCCAGUUUCGUCCUCGUGGAGGUCCCAGCAUGUCCAC--GCAAUAACGAUUGCGGGCAUAAUGCCCAUAAUGUCCUCGUAAUUACUGCCCA
.....((((((((((.....))).)))))))((((..((....((((((.((......)).)))))--(((((....)))))((((.....)))).....)....)).....)))).... ( -39.70)
>DroEre_CAF1 32571 117 + 1
ACGCCGCAAGGAGCCGCAGCGGCAUCCUUGCCAGUUUCGUCCUC-CGGAGGUCCCAGCAUGACCAC--GCAAUAACGAUUGCGGGCAUAAUGCCCAUAAUGUCCUCAUAAUUACUGCCCA
.....(((((((((((...)))).)))))))((((.........-.(((((((.......))))..--(((((....)))))((((.....))))......)))........)))).... ( -38.57)
>DroYak_CAF1 29669 118 + 1
ACGCCGCAAGGAGCCACAUCGGCAUCCUUGCCAGUUUCGUCCUCGUGGAGGUCCCAGCGUGUCCAC--GCAAUAACGAUUGCGGCCAUAAUGCCCAUAAUGUCCUCAUAAUUACUGCCCA
..(((((((((..((.....((((....)))).......(((....)))))..)).((((....))--))........)))))))................................... ( -34.80)
>consensus
ACGCCGCAAGGAGCCACAUCGGCAUCCUUGCCAGUUUCGUCCUCGUGGAGGUCCCAGCAUGUCCAC__GCAAUAACGAUUGCGGGCAUAAUGCCCAUAAUGUCCUCAUAAUUACUGCCCA
.....((((((((((.....))).)))))))((((...(.((((...)))).)...((((........(((((....)))))((((.....))))...))))..........)))).... (-35.04 = -35.08 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:58 2006