Locus 3901

Sequence ID	X_DroMel_CAF1
Location	10,446,967 – 10,447,110
Length	143
Max. P	0.965517

overview

Window 1

Location	10,446,967 – 10,447,081
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.31
Mean single sequence MFE	-28.26
Consensus MFE	-20.07
Energy contribution	-21.75
Covariance contribution	1.68
Combinations/Pair	1.07
Mean z-score	-1.98
Structure conservation index	0.71
SVM decision value	0.98
SVM RNA-class probability	0.893637
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10446967 114 - 22224390
UUGCGACUAUCUAUGAGUGAUUUCAAUUCCACCAC--CAAUAUU---UUUG-GCGUGGAAUUGGGAACACUCCCCUAAUGCGAUAUAUAAACGAAAGCUGACAACCCUAUUGUACCGCUC
..(((.........(((((.(..(((((((((..(--(((....---.)))-).)))))))))..).)))))......(((((((......(....)..........))))))).))).. ( -33.19)
>DroSec_CAF1 5509 110 - 1
UUGCGACAAUCUAUGAGUGAUUUCAAUUCCACCAC------ACU---UUUG-GCGUGGAAUUGGGAACACUCCCCUCAUGCGAUGUGUAAACGAAAGCUGACAACCCUAUUGGACCGCUC
..(((.((((....(((((.(..(((((((((..(------(..---..))-..)))))))))..).)))))...(((.((..(((....)))...))))).......))))...))).. ( -31.50)
>DroSim_CAF1 5490 110 - 1
UUGCGACAAUCUAUGAGUGAUUUCAAUUCCACCAC------ACU---UUUG-GCGUGGAAUUGGGAACACUCCCCUCAUGCGAUGUGUAAACGAAAGCUGACAACCCUAUUGGACCGCUC
..(((.((((....(((((.(..(((((((((..(------(..---..))-..)))))))))..).)))))...(((.((..(((....)))...))))).......))))...))).. ( -31.50)
>DroEre_CAF1 5780 115 - 1
CUGCUACAU----UUAGUGAUUUCAAUUCCACCACACCAACACCACAUUCG-AUGUGGAAUCGGGAACACUCCCCACAUGCGAUGUGUAACCAAACGCUGACAACCCUAUUGUACCGCUA
.(((.((((----(..(((.......................((((((...-))))))....((((....))))..)))..)))))))).......((.(((((.....)))).).)).. ( -20.70)
>DroYak_CAF1 6173 105 - 1
UUGCUA-------UUAGUGAUUUCAAUUCCACCAUACCA-CACU--GUUAAAUUGUGGAAUUGGGAACACUCCCCCCAUGCGAUGUGUAAGCAAACGCUGACAACCCUAUUGUG-----A
......-------..((((.(..(((((((((.((....-....--.....)).)))))))))..).))))........(((((((((.(((....))).)))....)))))).-----. ( -24.42)
>consensus
UUGCGACAAUCUAUGAGUGAUUUCAAUUCCACCAC__CA__ACU___UUUG_GCGUGGAAUUGGGAACACUCCCCUCAUGCGAUGUGUAAACGAAAGCUGACAACCCUAUUGUACCGCUC
..(((.........(((((.(..(((((((((......................)))))))))..).)))))......((((((((((...(....)...)))....))))))).))).. (-20.07 = -21.75 +   1.68)

alignment

secondary structure

dotplot

Window 2

Location	10,447,007 – 10,447,110
Length	103
Sequences	3
Columns	112
Reading direction	forward
Mean pairwise identity	88.25
Mean single sequence MFE	-28.53
Consensus MFE	-21.45
Energy contribution	-21.57
Covariance contribution	0.11
Combinations/Pair	1.04
Mean z-score	-2.02
Structure conservation index	0.75
SVM decision value	0.00
SVM RNA-class probability	0.533862
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10447007 103 + 22224390
CAUUAGGGGAGUGUUCCCAAUUCCACGCCAAAAAUAUUGGUGGUGGAAUUGAAAUCACUCAUAGAUAGUCGCAAUAUAAUUUGUUCUAUU---------GUGUGUAAUUUAA
........(((((....((((((((((((((.....))))).)))))))))....))))).(((((...(((((((.((....)).))))---------)))....))))). ( -30.70)
>DroSec_CAF1 5549 108 + 1
CAUGAGGGGAGUGUUCCCAAUUCCACGCCAAAAGU----GUGGUGGAAUUGAAAUCACUCAUAGAUUGUCGCAAUAUAAUUUAUUCUAUUGUGGGUAUUGUGUGUAAUUCGA
..((((..(((((....(((((((((..((....)----)..)))))))))....))))).........((((((((....((......))...)))))))).....)))). ( -27.00)
>DroSim_CAF1 5530 108 + 1
CAUGAGGGGAGUGUUCCCAAUUCCACGCCAAAAGU----GUGGUGGAAUUGAAAUCACUCAUAGAUUGUCGCAAUAUAAUUUAUUCUAUUGUGGGUUUUGUGUGUAAUUCGA
........(((((....(((((((((..((....)----)..)))))))))....)))))...(((((.((((....(((((((......)))))))...)))))))))... ( -27.90)
>consensus
CAUGAGGGGAGUGUUCCCAAUUCCACGCCAAAAGU____GUGGUGGAAUUGAAAUCACUCAUAGAUUGUCGCAAUAUAAUUUAUUCUAUUGUGGGU_UUGUGUGUAAUUCGA
....(((.(((((....(((((((((((...........)).)))))))))....)))))(((((((((......))))))))))))......................... (-21.45 = -21.57 +   0.11)

alignment

secondary structure

dotplot

Window 3

Location	10,447,007 – 10,447,110
Length	103
Sequences	3
Columns	112
Reading direction	reverse
Mean pairwise identity	88.25
Mean single sequence MFE	-26.20
Consensus MFE	-21.63
Energy contribution	-21.63
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.62
Structure conservation index	0.83
SVM decision value	1.58
SVM RNA-class probability	0.965517
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10447007 103 - 22224390
UUAAAUUACACAC---------AAUAGAACAAAUUAUAUUGCGACUAUCUAUGAGUGAUUUCAAUUCCACCACCAAUAUUUUUGGCGUGGAAUUGGGAACACUCCCCUAAUG
..........(.(---------((((..........))))).).........(((((.(..(((((((((..((((.....)))).)))))))))..).)))))........ ( -28.60)
>DroSec_CAF1 5549 108 - 1
UCGAAUUACACACAAUACCCACAAUAGAAUAAAUUAUAUUGCGACAAUCUAUGAGUGAUUUCAAUUCCACCAC----ACUUUUGGCGUGGAAUUGGGAACACUCCCCUCAUG
..((...............(.(((((..........))))).).........(((((.(..(((((((((..(----(....))..)))))))))..).)))))...))... ( -25.00)
>DroSim_CAF1 5530 108 - 1
UCGAAUUACACACAAAACCCACAAUAGAAUAAAUUAUAUUGCGACAAUCUAUGAGUGAUUUCAAUUCCACCAC----ACUUUUGGCGUGGAAUUGGGAACACUCCCCUCAUG
..((...............(.(((((..........))))).).........(((((.(..(((((((((..(----(....))..)))))))))..).)))))...))... ( -25.00)
>consensus
UCGAAUUACACACAA_ACCCACAAUAGAAUAAAUUAUAUUGCGACAAUCUAUGAGUGAUUUCAAUUCCACCAC____ACUUUUGGCGUGGAAUUGGGAACACUCCCCUCAUG
.......................(((((...................)))))(((((.(..((((((((((.............).)))))))))..).)))))........ (-21.63 = -21.63 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:18 2006