Locus 3538

Sequence ID	3L_DroMel_CAF1
Location	10,369,478 – 10,369,615
Length	137
Max. P	0.996992

overview

Window 2

Location	10,369,478 – 10,369,583
Length	105
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	93.05
Mean single sequence MFE	-37.08
Consensus MFE	-31.27
Energy contribution	-32.03
Covariance contribution	0.76
Combinations/Pair	1.03
Mean z-score	-2.47
Structure conservation index	0.84
SVM decision value	2.78
SVM RNA-class probability	0.996992
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10369478 105 + 23771897
CAUGCGUCUUUGAUUGCUUUGGCUUUGGCUUUGGCGUUGGCUUUUCAGUGGCCAUCGCUGC-----------UCUAUCGCCUUGCAACGUCGACAGUCGACGGCUAAAUACGCAAC
..(((((.((((.((((...(((..(((...(((((.(((((.......))))).))))).-----------.)))..)))..))))(((((.....)))))..)))).))))).. ( -39.30)
>DroSec_CAF1 243213 105 + 1
CAUGCGUCUUUGAUUGCUUUGGCUUUGGCUUUGCCGUUGUCUUUUCAGUGGCCAUCGCUGC-----------UCUAUUGCCUUGCAACGUCGACAGUCGACGGCUAAAUACGCAAC
..(((((.((((.((((...(((..(((....((.((.(((........))).)).))...-----------.)))..)))..))))(((((.....)))))..)))).))))).. ( -32.20)
>DroSim_CAF1 253899 105 + 1
CAUGCGUCUUUGAUUGCUUUGGCUUUGGCUUUGCCGUUGGCUUUUCAGUGGCCAUCGCUGC-----------UCUAUCGCCUUGCAACGUCGACAGUCGACGGCUAAAUACGCAAC
..(((((.((((.((((...(((..(((....((...(((((.......)))))..))...-----------.)))..)))..))))(((((.....)))))..)))).))))).. ( -35.20)
>DroEre_CAF1 257994 105 + 1
CAUGCGUCUUUGAUUGCUUUGGCUUUGGCUUUCGCGUUGGCUUUUCAGUGGCCAUCGCUGC-----------UCCAUCGCCUUGCAACGUCGACAGUCGACGGCUAAAUACGCAAC
..(((((.((((.((((...(((..(((.....(((.(((((.......))))).)))...-----------.)))..)))..))))(((((.....)))))..)))).))))).. ( -39.90)
>DroYak_CAF1 255616 116 + 1
CAUGCGUCUUUGAUUGCUUUAGCUUUGGCUUUGGCGUUGGCUUUUCAGUGGCCAUCGCUGCACCAACACUGCACCAUCGCCUUGCAACGUCGACAGUCGACGGCUAAAUACGCAAC
..(((((.((((...((....((...(((..(((((.(((((.......))))).)))((((.......)))).))..)))..))..(((((.....))))))))))).))))).. ( -38.80)
>consensus
CAUGCGUCUUUGAUUGCUUUGGCUUUGGCUUUGGCGUUGGCUUUUCAGUGGCCAUCGCUGC___________UCUAUCGCCUUGCAACGUCGACAGUCGACGGCUAAAUACGCAAC
..(((((.((((.((((...(((..(((....((((.(((((.......))))).))))..............)))..)))..))))(((((.....)))))..)))).))))).. (-31.27 = -32.03 +   0.76)

alignment

secondary structure

dotplot

Window 3

Location	10,369,515 – 10,369,615
Length	100
Sequences	5
Columns	111
Reading direction	forward
Mean pairwise identity	92.91
Mean single sequence MFE	-31.92
Consensus MFE	-28.42
Energy contribution	-28.62
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.59
Structure conservation index	0.89
SVM decision value	1.45
SVM RNA-class probability	0.955379
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10369515 100 + 23771897
UGGCUUUUCAGUGGCCAUCGCUGC-----------UCUAUCGCCUUGCAACGUCGACAGUCGACGGCUAAAUACGCAACACCAUCGGUGAGGGCCACGCCCUCAAAAAAGC
..((((((...(((((...((.((-----------......))...))...((((.....)))))))))..................(((((((...))))))).)))))) ( -30.90)
>DroSec_CAF1 243250 100 + 1
UGUCUUUUCAGUGGCCAUCGCUGC-----------UCUAUUGCCUUGCAACGUCGACAGUCGACGGCUAAAUACGCAACACCAUCGGUGAUGGCCACGCCCUCAAAAAAGC
..........(((((((((((((.-----------....((((.......(((((.....))))).........))))......))))))))))))).............. ( -34.79)
>DroSim_CAF1 253936 100 + 1
UGGCUUUUCAGUGGCCAUCGCUGC-----------UCUAUCGCCUUGCAACGUCGACAGUCGACGGCUAAAUACGCAACACCAUCGGUGAGGGCCACGCCCUCAAAAAAGC
..((((((...(((((...((.((-----------......))...))...((((.....)))))))))..................(((((((...))))))).)))))) ( -30.90)
>DroEre_CAF1 258031 99 + 1
UGGCUUUUCAGUGGCCAUCGCUGC-----------UCCAUCGCCUUGCAACGUCGACAGUCGACGGCUAAAUACGCAACACCAUCGGUGCGGGCCACGCCCUCAAA-AAGC
..((((((..((((((...(((((-----------...........))).(((((.....)))))))......((((.(......).)))))))))).......))-)))) ( -30.30)
>DroYak_CAF1 255653 111 + 1
UGGCUUUUCAGUGGCCAUCGCUGCACCAACACUGCACCAUCGCCUUGCAACGUCGACAGUCGACGGCUAAAUACGCAACACCAUCGGUGAGGGCCACGCCCUCAAAAAAGC
.(((......((((((...(.((((.......)))).).(((((......(((((.....)))))((.......)).........))))).)))))))))........... ( -32.70)
>consensus
UGGCUUUUCAGUGGCCAUCGCUGC___________UCUAUCGCCUUGCAACGUCGACAGUCGACGGCUAAAUACGCAACACCAUCGGUGAGGGCCACGCCCUCAAAAAAGC
..........((((((.((((((...........................(((((.....)))))((.......))........)))))).)))))).............. (-28.42 = -28.62 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	10,369,515 – 10,369,615
Length	100
Sequences	5
Columns	111
Reading direction	reverse
Mean pairwise identity	92.91
Mean single sequence MFE	-39.30
Consensus MFE	-32.32
Energy contribution	-32.36
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.64
Structure conservation index	0.82
SVM decision value	0.79
SVM RNA-class probability	0.851809
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10369515 100 - 23771897
GCUUUUUUGAGGGCGUGGCCCUCACCGAUGGUGUUGCGUAUUUAGCCGUCGACUGUCGACGUUGCAAGGCGAUAGA-----------GCAGCGAUGGCCACUGAAAAGCCA
(((((((((((.(((..((((........)).))..))).))))(((((((.(((((...(((((...))))).))-----------.))))))))))....))))))).. ( -37.10)
>DroSec_CAF1 243250 100 - 1
GCUUUUUUGAGGGCGUGGCCAUCACCGAUGGUGUUGCGUAUUUAGCCGUCGACUGUCGACGUUGCAAGGCAAUAGA-----------GCAGCGAUGGCCACUGAAAAGACA
(((((....)))))((((((((((((...)))(((((..........((((.....))))(((((...)))))...-----------)))))))))))))).......... ( -38.00)
>DroSim_CAF1 253936 100 - 1
GCUUUUUUGAGGGCGUGGCCCUCACCGAUGGUGUUGCGUAUUUAGCCGUCGACUGUCGACGUUGCAAGGCGAUAGA-----------GCAGCGAUGGCCACUGAAAAGCCA
(((((((((((.(((..((((........)).))..))).))))(((((((.(((((...(((((...))))).))-----------.))))))))))....))))))).. ( -37.10)
>DroEre_CAF1 258031 99 - 1
GCUU-UUUGAGGGCGUGGCCCGCACCGAUGGUGUUGCGUAUUUAGCCGUCGACUGUCGACGUUGCAAGGCGAUGGA-----------GCAGCGAUGGCCACUGAAAAGCCA
((((-(((.((.(((..(((((......))).))..))).....(((((((.(((.(..((((((...))))))..-----------)))))))))))..))))))))).. ( -41.20)
>DroYak_CAF1 255653 111 - 1
GCUUUUUUGAGGGCGUGGCCCUCACCGAUGGUGUUGCGUAUUUAGCCGUCGACUGUCGACGUUGCAAGGCGAUGGUGCAGUGUUGGUGCAGCGAUGGCCACUGAAAAGCCA
(((((((((((.(((..((((........)).))..))).))))(((((((.((((((((((((((.........))))))))))..)))))))))))....))))))).. ( -43.10)
>consensus
GCUUUUUUGAGGGCGUGGCCCUCACCGAUGGUGUUGCGUAUUUAGCCGUCGACUGUCGACGUUGCAAGGCGAUAGA___________GCAGCGAUGGCCACUGAAAAGCCA
((((......))))((((((.(((((...)))(((((..........((((.....))))(((((...)))))..............))))))).)))))).......... (-32.32 = -32.36 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:33 2006