Locus 3916

Sequence ID	2L_DroMel_CAF1
Location	11,427,955 – 11,428,088
Length	133
Max. P	0.996244

overview

Window 3

Location	11,427,955 – 11,428,048
Length	93
Sequences	6
Columns	93
Reading direction	forward
Mean pairwise identity	94.12
Mean single sequence MFE	-23.78
Consensus MFE	-21.65
Energy contribution	-21.48
Covariance contribution	-0.16
Combinations/Pair	1.22
Mean z-score	-1.08
Structure conservation index	0.91
SVM decision value	0.13
SVM RNA-class probability	0.598642
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11427955 93 + 22407834
ACAAAUGUUUCGCGCUUUUCGGGCCAAUUCAAUGAAUUUUCGGCUAACUGUUGAUGCUGCGGUUAUUUUGCAGCCUCGGCUCGCAUCAAUUAA
...........(((.......(((((((((...)))))...))))....(((((.(((((((.....))))))).))))).)))......... ( -24.30)
>DroSec_CAF1 145489 93 + 1
AGAAAUGUUUCGCGCAGUUCGGGCCAAUUCAAUGCAUUUUCGGCUAACUGUUGAUGCUGCGGUUAUUUUGCAGCCUCGGCUCGCAUCAAUUAA
...........(((.(((..((((.........(((((..(((....)))..)))))(((((.....)))))))))..))))))......... ( -26.30)
>DroSim_CAF1 153022 93 + 1
ACAAAUGUUUCGCGCUGUUCGGGCCAAUUCAAUGCAUUUUCGGCUAACUGUUGAUGCUGCGGUUAUUUUGCAGCCUCGGCUCGCAUCAAUUAA
...........(((..((..((((.........(((((..(((....)))..)))))(((((.....)))))))))..)).)))......... ( -24.10)
>DroEre_CAF1 153107 92 + 1
ACAAAUGUUUCGCGCUGUUCGGGCCAAUUCAAUGAAUUUUCGGCUAACUGUUGAUGCUGCGGUUAUU-UGCAGCCUCGGCUCGCAUCAAUUAA
...........(((.......(((((((((...)))))...))))....(((((.(((((((....)-)))))).))))).)))......... ( -24.30)
>DroYak_CAF1 150931 92 + 1
-CAAAUGUUUCGCGCUGUUCGGGCCAAUUCAAUGAAUUUUCGGCUAACUGUUGAUGCUGCAGUUAUUCUGCAGCCUCGGCUCGCAUCAAUUAA
-..........(((.......(((((((((...)))))...))))....(((((.(((((((.....))))))).))))).)))......... ( -27.00)
>DroAna_CAF1 130965 93 + 1
ACAAAUGUUUCGCACUGUUUGGGCCAAUUCAAUGAAUUUUCGGCUAACUGUUGAUGUUGCGGUUAUUUUCCAAAGUCGGCUCGCACCAAUUAA
.....(((...((....(((((((((((((...)))))...)))(((((((.......)))))))....)))))....))..)))........ ( -16.70)
>consensus
ACAAAUGUUUCGCGCUGUUCGGGCCAAUUCAAUGAAUUUUCGGCUAACUGUUGAUGCUGCGGUUAUUUUGCAGCCUCGGCUCGCAUCAAUUAA
...................((((((..............(((((.....))))).(((((((.....)))))))...)))))).......... (-21.65 = -21.48 +  -0.16)

alignment

secondary structure

dotplot

Window 4

Location	11,427,986 – 11,428,088
Length	102
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	94.38
Mean single sequence MFE	-37.02
Consensus MFE	-33.27
Energy contribution	-33.61
Covariance contribution	0.34
Combinations/Pair	1.13
Mean z-score	-2.37
Structure conservation index	0.90
SVM decision value	2.67
SVM RNA-class probability	0.996244
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11427986 102 + 22407834
AUGAAUUUUCGGCUAACUGUUGAUGCUGCGGUUAUUUUGCAGCCUCGGCUCGCAUCAAUUAAGAGGUGUGCUGCACGGGCCGAGUCAAUUAAGCUGCCGGCA
........(((((.....(((((.(((((((.....)))))))((((((((...((......)).(((.....))))))))))))))))......))))).. ( -37.30)
>DroSec_CAF1 145520 102 + 1
AUGCAUUUUCGGCUAACUGUUGAUGCUGCGGUUAUUUUGCAGCCUCGGCUCGCAUCAAUUAAGAGGUGCGCUGCACGGGCCGAGUCAAUUAAGCUGCAGGCA
.(((.....(((((....(((((.(((((((.....)))))))(((((((((((((........)))))(.....))))))))))))))..)))))...))) ( -39.40)
>DroSim_CAF1 153053 102 + 1
AUGCAUUUUCGGCUAACUGUUGAUGCUGCGGUUAUUUUGCAGCCUCGGCUCGCAUCAAUUAAGAGGUGUGCUGCACGGGCCGAGUCAAUUAAGCUGCCGGCA
........(((((.....(((((.(((((((.....)))))))((((((((...((......)).(((.....))))))))))))))))......))))).. ( -37.30)
>DroEre_CAF1 153138 100 + 1
AUGAAUUUUCGGCUAACUGUUGAUGCUGCGGUUAUU-UGCAGCCUCGGCUCGCAUCAAUUAAGAGGUGUGCUGCACG-GCCGAGUCAAUUAAGCUGCCGGCA
........(((((.....(((((.(((((((....)-))))))(((((((((((((........))))))......)-)))))))))))......))))).. ( -36.60)
>DroYak_CAF1 150961 102 + 1
AUGAAUUUUCGGCUAACUGUUGAUGCUGCAGUUAUUCUGCAGCCUCGGCUCGCAUCAAUUAAGAGGUGUGUUGCACGGGCCGAGUCAAUUAAGCUGCCGGCA
........(((((.....(((((.(((((((.....)))))))(((((((((((((........)))))(.....))))))))))))))......))))).. ( -40.20)
>DroAna_CAF1 130996 99 + 1
AUGAAUUUUCGGCUAACUGUUGAUGUUGCGGUUAUUUUCCAAAGUCGGCUCGCACCAAUUAAGAGGUGU---GCACGGGCCGAGUCAAUUAAGCUGCCGGCA
........(((((.....((((((.....((.......))....((((((((((((........)))).---...))))))))))))))......))))).. ( -31.30)
>consensus
AUGAAUUUUCGGCUAACUGUUGAUGCUGCGGUUAUUUUGCAGCCUCGGCUCGCAUCAAUUAAGAGGUGUGCUGCACGGGCCGAGUCAAUUAAGCUGCCGGCA
........(((((.....(((((.(((((((.....)))))))(((((((((((((........)))).......))))))))))))))......))))).. (-33.27 = -33.61 +   0.34)

alignment

secondary structure

dotplot

Window 5

Location	11,427,986 – 11,428,088
Length	102
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	94.38
Mean single sequence MFE	-32.53
Consensus MFE	-28.55
Energy contribution	-29.17
Covariance contribution	0.61
Combinations/Pair	1.07
Mean z-score	-2.43
Structure conservation index	0.88
SVM decision value	2.23
SVM RNA-class probability	0.990766
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11427986 102 - 22407834
UGCCGGCAGCUUAAUUGACUCGGCCCGUGCAGCACACCUCUUAAUUGAUGCGAGCCGAGGCUGCAAAAUAACCGCAGCAUCAACAGUUAGCCGAAAAUUCAU
...((((((((...((((((((((...((((.((...........)).)))).))))))(((((.........))))).)))).)))).))))......... ( -33.40)
>DroSec_CAF1 145520 102 - 1
UGCCUGCAGCUUAAUUGACUCGGCCCGUGCAGCGCACCUCUUAAUUGAUGCGAGCCGAGGCUGCAAAAUAACCGCAGCAUCAACAGUUAGCCGAAAAUGCAU
(((...(.(((.(((((.((((((.(((((...)))).((......))...).))))))(((((.........))))).....)))))))).).....))). ( -30.60)
>DroSim_CAF1 153053 102 - 1
UGCCGGCAGCUUAAUUGACUCGGCCCGUGCAGCACACCUCUUAAUUGAUGCGAGCCGAGGCUGCAAAAUAACCGCAGCAUCAACAGUUAGCCGAAAAUGCAU
(((((((((((...((((((((((...((((.((...........)).)))).))))))(((((.........))))).)))).)))).)))).....))). ( -33.60)
>DroEre_CAF1 153138 100 - 1
UGCCGGCAGCUUAAUUGACUCGGC-CGUGCAGCACACCUCUUAAUUGAUGCGAGCCGAGGCUGCA-AAUAACCGCAGCAUCAACAGUUAGCCGAAAAUUCAU
...((((((((...((((((((((-..((((.((...........)).)))).))))))(((((.-.......))))).)))).)))).))))......... ( -34.10)
>DroYak_CAF1 150961 102 - 1
UGCCGGCAGCUUAAUUGACUCGGCCCGUGCAACACACCUCUUAAUUGAUGCGAGCCGAGGCUGCAGAAUAACUGCAGCAUCAACAGUUAGCCGAAAAUUCAU
...((((((((...((((((((((.(((((((............))).)))).))))))(((((((.....))))))).)))).)))).))))......... ( -38.20)
>DroAna_CAF1 130996 99 - 1
UGCCGGCAGCUUAAUUGACUCGGCCCGUGC---ACACCUCUUAAUUGGUGCGAGCCGACUUUGGAAAAUAACCGCAACAUCAACAGUUAGCCGAAAAUUCAU
...((((((((...((((.(((((.((...---.((((........)))))).)))))....((.......))......)))).)))).))))......... ( -25.30)
>consensus
UGCCGGCAGCUUAAUUGACUCGGCCCGUGCAGCACACCUCUUAAUUGAUGCGAGCCGAGGCUGCAAAAUAACCGCAGCAUCAACAGUUAGCCGAAAAUUCAU
...((((((((...((((((((((.(((((((............))).)))).))))))(((((.........))))).)))).)))).))))......... (-28.55 = -29.17 +   0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:42 2006