Locus 4726

Sequence ID	2L_DroMel_CAF1
Location	13,548,593 – 13,548,744
Length	151
Max. P	0.978104

overview

Window 5

Location	13,548,593 – 13,548,704
Length	111
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	96.23
Mean single sequence MFE	-41.62
Consensus MFE	-37.72
Energy contribution	-37.48
Covariance contribution	-0.24
Combinations/Pair	1.08
Mean z-score	-1.64
Structure conservation index	0.91
SVM decision value	1.59
SVM RNA-class probability	0.966009
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13548593 111 + 22407834
GUGGCAGAGCCGAGGUGCCGUGGAAUGGGGA-UUUUCCCGAAAAGUAACGGCUCUUUCGGGAAAAACCGUUUUCCGUAUUGAUUUCGGGGGGCGCUGCAUGUGAGCUUCCCA
..(((...)))(((((....(((((.(.((.-((((((((((((((....))).))))))))))).)).).))))).....)))))(((((((.(.......).))))))). ( -42.10)
>DroSec_CAF1 7453 111 + 1
GUGGCAGAGCCGAGGAGCCGUGGAAUGGGGA-UUUUCCCGAACAGUAACGGCUCUUUCGGGAAAAACCGUUUUCCGUAUUGAUUUCGGGGGGCGCUGCAUGUGAGCUUCCCA
..(((...)))((((((((((.(..(((((.-...)))))..)....)))))))))).(((((.....(((..(((.........)))..)))(((.......)))))))). ( -41.50)
>DroSim_CAF1 7679 112 + 1
GUGGCAGAGCCGAGGAGCCGUGGAAUGGGUACUUUUCCCGAAAAGUAACGGCUCUUUCGGGAAAAACCGUUUUCCGUAUUGAUUUCGGGGGGCGCUGCAUGUGAGCUUCCCA
..(((...)))((((((((((....((((.......)))).......)))))))))).(((((.....(((..(((.........)))..)))(((.......)))))))). ( -40.40)
>DroEre_CAF1 9795 110 + 1
GUGGCAGAGCCGAGGAGCAAUGGAACGGGGA-UU-UCCCGAAAAGUAACGGCUCUUUCGGGAAAAACCGUUUUCCGUAUUGAUUUCGGGGGGCGCUGCAUGUGAGCUUCCCA
.((((...)))).(((((((((((((((...-((-(((((((((((....))).))))))))))..))))..)))))..)).))))(((((((.(.......).))))))). ( -42.30)
>DroYak_CAF1 7771 111 + 1
GUGGCAGAGCCGAGGAGCAAUGGAACGGGGA-UUUUCCCGAAAAGUAACGGCUCUUUCGGGAAAAACCGUUUUCCGUAUUGAUUUCGGGGGGCGCUGCAUGUGAGCUUUCCA
.(((.(((((((.(.(((..........((.-((((((((((((((....))).))))))))))).))(((..(((.........)))..)))))).)...)).)))))))) ( -41.80)
>consensus
GUGGCAGAGCCGAGGAGCCGUGGAAUGGGGA_UUUUCCCGAAAAGUAACGGCUCUUUCGGGAAAAACCGUUUUCCGUAUUGAUUUCGGGGGGCGCUGCAUGUGAGCUUCCCA
..(((...)))((((....(((((((((....((((((((((((((....))).))))))))))).))))..))))).....))))(((((((.(.......).))))))). (-37.72 = -37.48 +  -0.24)

alignment

secondary structure

dotplot

Window 6

Location	13,548,593 – 13,548,704
Length	111
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	96.23
Mean single sequence MFE	-33.09
Consensus MFE	-28.76
Energy contribution	-29.16
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.71
Structure conservation index	0.87
SVM decision value	1.25
SVM RNA-class probability	0.936629
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13548593 111 - 22407834
UGGGAAGCUCACAUGCAGCGCCCCCCGAAAUCAAUACGGAAAACGGUUUUUCCCGAAAGAGCCGUUACUUUUCGGGAAAA-UCCCCAUUCCACGGCACCUCGGCUCUGCCAC
.(((..((((....).)))..))).............((((...((.((((((((((.(((......)))))))))))))-.))...))))..((((.........)))).. ( -33.10)
>DroSec_CAF1 7453 111 - 1
UGGGAAGCUCACAUGCAGCGCCCCCCGAAAUCAAUACGGAAAACGGUUUUUCCCGAAAGAGCCGUUACUGUUCGGGAAAA-UCCCCAUUCCACGGCUCCUCGGCUCUGCCAC
.(((..((((....).)))..)))(((.........))).....(((.....((((..(((((((........(((....-.)))......))))))).))))....))).. ( -33.04)
>DroSim_CAF1 7679 112 - 1
UGGGAAGCUCACAUGCAGCGCCCCCCGAAAUCAAUACGGAAAACGGUUUUUCCCGAAAGAGCCGUUACUUUUCGGGAAAAGUACCCAUUCCACGGCUCCUCGGCUCUGCCAC
.(((..((((....).)))..)))(((.........))).....(((.....((((..((((((((((((((....)))))))........))))))).))))....))).. ( -32.70)
>DroEre_CAF1 9795 110 - 1
UGGGAAGCUCACAUGCAGCGCCCCCCGAAAUCAAUACGGAAAACGGUUUUUCCCGAAAGAGCCGUUACUUUUCGGGA-AA-UCCCCGUUCCAUUGCUCCUCGGCUCUGCCAC
.(((..((((....).)))..)))((((...((((..((((...((..(((((((((.(((......))))))))))-))-..))..))))))))....))))......... ( -33.80)
>DroYak_CAF1 7771 111 - 1
UGGAAAGCUCACAUGCAGCGCCCCCCGAAAUCAAUACGGAAAACGGUUUUUCCCGAAAGAGCCGUUACUUUUCGGGAAAA-UCCCCGUUCCAUUGCUCCUCGGCUCUGCCAC
..............((((.(((....((...((((..((((...((.((((((((((.(((......)))))))))))))-.))...)))))))).))...))).))))... ( -32.80)
>consensus
UGGGAAGCUCACAUGCAGCGCCCCCCGAAAUCAAUACGGAAAACGGUUUUUCCCGAAAGAGCCGUUACUUUUCGGGAAAA_UCCCCAUUCCACGGCUCCUCGGCUCUGCCAC
..............((((.(((....(....).....((((...((.((((((((((.(((......)))))))))))))...))..))))..........))).))))... (-28.76 = -29.16 +   0.40)

alignment

secondary structure

dotplot

Window 7

Location	13,548,624 – 13,548,744
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.67
Mean single sequence MFE	-34.97
Consensus MFE	-33.99
Energy contribution	-34.39
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.70
Structure conservation index	0.97
SVM decision value	1.81
SVM RNA-class probability	0.978104
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13548624 120 - 22407834
ACUCCUUUCAUCGGGCGUUUUAGAAUGCAUAUUUGGUUUAUGGGAAGCUCACAUGCAGCGCCCCCCGAAAUCAAUACGGAAAACGGUUUUUCCCGAAAGAGCCGUUACUUUUCGGGAAAA
............((((((.......(((((....(((((.....)))))...)))))))))))(((((((((......)).((((((((((.....))))))))))...))))))).... ( -35.21)
>DroSec_CAF1 7484 120 - 1
ACUCCUUUCAUCGGGCGUUUUAGAAUGCAUAUUUGGUUUAUGGGAAGCUCACAUGCAGCGCCCCCCGAAAUCAAUACGGAAAACGGUUUUUCCCGAAAGAGCCGUUACUGUUCGGGAAAA
............((((((.......(((((....(((((.....)))))...)))))))))))(((((.......((((..((((((((((.....)))))))))).))))))))).... ( -35.12)
>DroSim_CAF1 7711 120 - 1
ACUCCUUUCAUCGGGCGUUUUAGAAUGCAUAUUUGGUUUAUGGGAAGCUCACAUGCAGCGCCCCCCGAAAUCAAUACGGAAAACGGUUUUUCCCGAAAGAGCCGUUACUUUUCGGGAAAA
............((((((.......(((((....(((((.....)))))...)))))))))))(((((((((......)).((((((((((.....))))))))))...))))))).... ( -35.21)
>DroEre_CAF1 9826 119 - 1
ACUCCUUUCAUCGGGCGUUUUAGAAUGCAUAUUUCGUUUAUGGGAAGCUCACAUGCAGCGCCCCCCGAAAUCAAUACGGAAAACGGUUUUUCCCGAAAGAGCCGUUACUUUUCGGGA-AA
............(((((((......(.((((.......)))).)..((......)))))))))(((((((((......)).((((((((((.....))))))))))...))))))).-.. ( -34.20)
>DroYak_CAF1 7802 120 - 1
ACUCCUUUCAUCGGGCGUUUUAGAAUGCAUAUUUGGUUUAUGGAAAGCUCACAUGCAGCGCCCCCCGAAAUCAAUACGGAAAACGGUUUUUCCCGAAAGAGCCGUUACUUUUCGGGAAAA
............((((((.......(((((....(((((.....)))))...)))))))))))(((((((((......)).((((((((((.....))))))))))...))))))).... ( -35.11)
>consensus
ACUCCUUUCAUCGGGCGUUUUAGAAUGCAUAUUUGGUUUAUGGGAAGCUCACAUGCAGCGCCCCCCGAAAUCAAUACGGAAAACGGUUUUUCCCGAAAGAGCCGUUACUUUUCGGGAAAA
............((((((.......(((((....(((((.....)))))...)))))))))))(((((((((......)).((((((((((.....))))))))))...))))))).... (-33.99 = -34.39 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:40 2006