Locus 5320

Sequence ID	2R_DroMel_CAF1
Location	17,242,517 – 17,242,656
Length	139
Max. P	0.999976

overview

Window 8

Location	17,242,517 – 17,242,616
Length	99
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	96.04
Mean single sequence MFE	-35.46
Consensus MFE	-33.92
Energy contribution	-34.16
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-3.08
Structure conservation index	0.96
SVM decision value	5.12
SVM RNA-class probability	0.999974
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17242517 99 + 20766785
UGCAGUGGCAAAUUGUUUGGG-----CCCCCUUUGUUAGUGUUGCUGCAACAAGCUGCUGUUAUUGUUGCAACUUGCAACCGGCAGCUGCCUUUUCGAGUUUGU
(((((..(((........((.-----...))........)))..)))))...((((((((.....(((((.....)))))))))))))................ ( -35.09)
>DroSec_CAF1 42153 99 + 1
UGCAGUGGCAAAUUGUUUGGG-----CCCCCUUUGUUAUUGUUGCUGCAAAAAGCUGCUGUUAUUGUUGCAACUUGCCACCGGCAGCUGCCUUUUCGAGUUUGU
(((((..((((.......((.-----...)).......))))..)))))...((((((((.....((.((.....)).))))))))))................ ( -30.94)
>DroSim_CAF1 45182 99 + 1
UGCAGUGGCAAAUUGUUUGGG-----CCCCCUUUGUUAUUGUUGCUGCAACAAGCUGCUGUUAUUGUUGCAACUUGCAACCGGCAGCUGCCUUUUCGAGUUUGU
(((((..((((.......((.-----...)).......))))..)))))...((((((((.....(((((.....)))))))))))))................ ( -35.04)
>DroEre_CAF1 44413 99 + 1
UGCAGUGGCAAAUUGUUUGGG-----CCCCCAUUGUUAUUGUUGCUGCAACAAGCUGCUGUUAUUGUUGCAACUUGCAACCGGCAGCUGCCUUUUCGAGUUUGU
(((((..((((......(((.-----...)))......))))..)))))...((((((((.....(((((.....)))))))))))))................ ( -36.60)
>DroYak_CAF1 43597 104 + 1
UGCAGUGGCAAAUUGUUUGGGGGGCCCCCUCUUUGUUAUUGUUGCUGCAACAAGCUGCUGUUAUUGUUGCAACUUGCAACCGGCAGCUGCCUUUUCGAGUUUGU
(((((..((((.......(((((....)))))......))))..)))))...((((((((.....(((((.....)))))))))))))................ ( -39.62)
>consensus
UGCAGUGGCAAAUUGUUUGGG_____CCCCCUUUGUUAUUGUUGCUGCAACAAGCUGCUGUUAUUGUUGCAACUUGCAACCGGCAGCUGCCUUUUCGAGUUUGU
(((((..((((.......(((.......))).......))))..)))))...((((((((.....(((((.....)))))))))))))................ (-33.92 = -34.16 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	17,242,517 – 17,242,616
Length	99
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	96.04
Mean single sequence MFE	-30.08
Consensus MFE	-28.76
Energy contribution	-28.96
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-3.17
Structure conservation index	0.96
SVM decision value	5.16
SVM RNA-class probability	0.999976
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17242517 99 - 20766785
ACAAACUCGAAAAGGCAGCUGCCGGUUGCAAGUUGCAACAAUAACAGCAGCUUGUUGCAGCAACACUAACAAAGGGGG-----CCCAAACAAUUUGCCACUGCA
.............(((((((((.....(((((((((..........))))))))).)))))............((...-----.))........))))...... ( -29.20)
>DroSec_CAF1 42153 99 - 1
ACAAACUCGAAAAGGCAGCUGCCGGUGGCAAGUUGCAACAAUAACAGCAGCUUUUUGCAGCAACAAUAACAAAGGGGG-----CCCAAACAAUUUGCCACUGCA
.............(((....)))((((((((((((...........((.((.....)).))............((...-----.))...))))))))))))... ( -29.20)
>DroSim_CAF1 45182 99 - 1
ACAAACUCGAAAAGGCAGCUGCCGGUUGCAAGUUGCAACAAUAACAGCAGCUUGUUGCAGCAACAAUAACAAAGGGGG-----CCCAAACAAUUUGCCACUGCA
.............(((((((((.....(((((((((..........))))))))).)))))............((...-----.))........))))...... ( -29.20)
>DroEre_CAF1 44413 99 - 1
ACAAACUCGAAAAGGCAGCUGCCGGUUGCAAGUUGCAACAAUAACAGCAGCUUGUUGCAGCAACAAUAACAAUGGGGG-----CCCAAACAAUUUGCCACUGCA
.............(((((((((.....(((((((((..........))))))))).)))))...........(((...-----.))).......))))...... ( -30.00)
>DroYak_CAF1 43597 104 - 1
ACAAACUCGAAAAGGCAGCUGCCGGUUGCAAGUUGCAACAAUAACAGCAGCUUGUUGCAGCAACAAUAACAAAGAGGGGGCCCCCCAAACAAUUUGCCACUGCA
.............(((((((((.....(((((((((..........))))))))).)))))..............((((...))))........))))...... ( -32.80)
>consensus
ACAAACUCGAAAAGGCAGCUGCCGGUUGCAAGUUGCAACAAUAACAGCAGCUUGUUGCAGCAACAAUAACAAAGGGGG_____CCCAAACAAUUUGCCACUGCA
.............(((((((((.....(((((((((..........))))))))).)))))..............(((.....)))........))))...... (-28.76 = -28.96 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	17,242,541 – 17,242,656
Length	115
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	98.26
Mean single sequence MFE	-26.02
Consensus MFE	-24.82
Energy contribution	-25.22
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.66
Structure conservation index	0.95
SVM decision value	1.66
SVM RNA-class probability	0.970797
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17242541 115 - 20766785
AAACACGAAAACCUGCAUAAGCGAUGUUCCAACUCACCUGACAAACUCGAAAAGGCAGCUGCCGGUUGCAAGUUGCAACAAUAACAGCAGCUUGUUGCAGCAACACUAACAAAGG
...........(((((.....(((.(((.....((....))..)))))).....)).(((((.....(((((((((..........))))))))).)))))...........))) ( -26.40)
>DroSec_CAF1 42177 115 - 1
AAACACGAAAACCUGCAUAAGCGAUGUUCCAACUCACCUGACAAACUCGAAAAGGCAGCUGCCGGUGGCAAGUUGCAACAAUAACAGCAGCUUUUUGCAGCAACAAUAACAAAGG
............(((((.((((..((((.((((((((((((.....)))....(((....)))))))...))))).)))).........))))..)))))............... ( -24.70)
>DroSim_CAF1 45206 115 - 1
AAACACGAAAACCUGCAUAAGCGAUGUUCCAACUCACCUGACAAACUCGAAAAGGCAGCUGCCGGUUGCAAGUUGCAACAAUAACAGCAGCUUGUUGCAGCAACAAUAACAAAGG
...........(((((.....(((.(((.....((....))..)))))).....)).(((((.....(((((((((..........))))))))).)))))...........))) ( -26.40)
>DroEre_CAF1 44437 115 - 1
AAACACGAAAACCUGCAUAAGCGAUGUUCCAACUCACCUGACAAACUCGAAAAGGCAGCUGCCGGUUGCAAGUUGCAACAAUAACAGCAGCUUGUUGCAGCAACAAUAACAAUGG
............((((((((((..((((.........................(((....))).(((((.....)))))...))))...))))).)))))............... ( -26.30)
>DroYak_CAF1 43626 115 - 1
AAACACGAAAACCUGCAUAAGCGAUGUUCCAACUCACCUGACAAACUCGAAAAGGCAGCUGCCGGUUGCAAGUUGCAACAAUAACAGCAGCUUGUUGCAGCAACAAUAACAAAGA
............((((((((((..((((.........................(((....))).(((((.....)))))...))))...))))).)))))............... ( -26.30)
>consensus
AAACACGAAAACCUGCAUAAGCGAUGUUCCAACUCACCUGACAAACUCGAAAAGGCAGCUGCCGGUUGCAAGUUGCAACAAUAACAGCAGCUUGUUGCAGCAACAAUAACAAAGG
............((((((((((..((((.........................(((....))).(((((.....)))))...))))...))))).)))))............... (-24.82 = -25.22 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:01 2006