Locus 1046

Sequence ID	2R_DroMel_CAF1
Location	4,305,901 – 4,306,035
Length	134
Max. P	0.991877

overview

Window 0

Location	4,305,901 – 4,306,001
Length	100
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	81.32
Mean single sequence MFE	-32.88
Consensus MFE	-21.95
Energy contribution	-23.28
Covariance contribution	1.34
Combinations/Pair	1.20
Mean z-score	-1.99
Structure conservation index	0.67
SVM decision value	0.56
SVM RNA-class probability	0.781408
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4305901 100 + 20766785
CCUGCUCCCUUCCACCUUUCCAUGGACGUUUGCCCUUCAGUGACCUGAGAACUUUCCGGUAUUUAAUAUACUCGAAAGUACUUGGG-------------------GUGGAGUGGUGGAG
..........((((((.((((((((........))........((..((.((((((.(((((.....))))).)))))).))..))-------------------)))))).)))))). ( -37.80)
>DroSec_CAF1 61112 99 + 1
CCUGCUCCCUUCCAC-UUUCCAUGGACGUUUGCCCUUCAGUGACCUGAGAACUUUCCGGUAUUUAAUAUACUCGAAAGUACUUGGG-------------------GUGGAGUGGUGGAG
....((((...((((-..(((((((........))........((..((.((((((.(((((.....))))).)))))).))..))-------------------))))))))).)))) ( -34.80)
>DroSim_CAF1 64508 99 + 1
CCUGCUCCCUUCCAC-UUUCCAUGGACGUUUGCCCUUCAGUGACCGGAGAACUUUCCGGUAUUUAAUAUACUCGAAAGUACUUGGG-------------------GUGGAGUGGUGGAG
....((((...((((-..(((((((........))........((.(((.((((((.(((((.....))))).)))))).))).))-------------------))))))))).)))) ( -33.60)
>DroEre_CAF1 60417 91 + 1
CGUGUUCCCUUCCAC-UUUCCAUGGACGUUUGCCCUUCAGUGACCUGAGAACUUUCCGGCAUUUAAUAUACUCCAAAGUACUUGGG-------------------GU--------GGAG
.(((........)))-..(((.........((((..((((....))))((....)).))))........(((((((.....)))))-------------------))--------))). ( -18.10)
>DroYak_CAF1 61908 99 + 1
CAUGUUCCCUCCCAC-UUUCCAUGGACGUUUGCCCUUCAGUGACCUGAGAACUUUCCGGUAUUUAAUAUACUCGAAAGUACUUGGG-------------------GUGGAAUGGUGGAG
...........((((-(((((((((........))........((..((.((((((.(((((.....))))).)))))).))..))-------------------)))))).))))).. ( -33.30)
>DroAna_CAF1 69140 115 + 1
U---UUUCCAAAUAU-UUUCCUCGGUCGCUUGCCCUUCAGCGACCUGAGAACUUUUCGGUAUUUAAUAUACUGCCAGGUGCUUUGGCGGUUAUUGGGCAGAGGGUGUGGAGUGGAGAAG
(---((((((..(((-..((((((((((((........)))))))................(((((((.((((((((.....)))))))))))))))..))))).)))...))))))). ( -39.70)
>consensus
CCUGCUCCCUUCCAC_UUUCCAUGGACGUUUGCCCUUCAGUGACCUGAGAACUUUCCGGUAUUUAAUAUACUCGAAAGUACUUGGG___________________GUGGAGUGGUGGAG
....((((...((((...(((((((........))........((..((.((((((.(((((.....))))).)))))).))..))...................))))))))).)))) (-21.95 = -23.28 +   1.34)

alignment

secondary structure

dotplot

Window 1

Location	4,305,901 – 4,306,001
Length	100
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	81.32
Mean single sequence MFE	-28.91
Consensus MFE	-16.88
Energy contribution	-19.05
Covariance contribution	2.17
Combinations/Pair	1.10
Mean z-score	-1.83
Structure conservation index	0.58
SVM decision value	-0.02
SVM RNA-class probability	0.523417
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4305901 100 - 20766785
CUCCACCACUCCAC-------------------CCCAAGUACUUUCGAGUAUAUUAAAUACCGGAAAGUUCUCAGGUCACUGAAGGGCAAACGUCCAUGGAAAGGUGGAAGGGAGCAGG
((((.....(((((-------------------((((.(.((((((..((((.....))))..)))))).)((((....)))).((((....)))).)))...))))))..)))).... ( -32.30)
>DroSec_CAF1 61112 99 - 1
CUCCACCACUCCAC-------------------CCCAAGUACUUUCGAGUAUAUUAAAUACCGGAAAGUUCUCAGGUCACUGAAGGGCAAACGUCCAUGGAAA-GUGGAAGGGAGCAGG
((((.((((((((.-------------------.....(.((((((..((((.....))))..)))))).)((((....)))).((((....)))).))))..-))))...)))).... ( -30.30)
>DroSim_CAF1 64508 99 - 1
CUCCACCACUCCAC-------------------CCCAAGUACUUUCGAGUAUAUUAAAUACCGGAAAGUUCUCCGGUCACUGAAGGGCAAACGUCCAUGGAAA-GUGGAAGGGAGCAGG
((((.((((((((.-------------------.....(((((....))))).......((((((......)))))).......((((....)))).))))..-))))...)))).... ( -30.00)
>DroEre_CAF1 60417 91 - 1
CUCC--------AC-------------------CCCAAGUACUUUGGAGUAUAUUAAAUGCCGGAAAGUUCUCAGGUCACUGAAGGGCAAACGUCCAUGGAAA-GUGGAAGGGAACACG
.(((--------..-------------------.(((((...))))).((((.....)))).)))..((((((...(((((...((((....))))......)-))))..))))))... ( -22.80)
>DroYak_CAF1 61908 99 - 1
CUCCACCAUUCCAC-------------------CCCAAGUACUUUCGAGUAUAUUAAAUACCGGAAAGUUCUCAGGUCACUGAAGGGCAAACGUCCAUGGAAA-GUGGGAGGGAACAUG
.(((....((((((-------------------.(((.(.((((((..((((.....))))..)))))).)((((....)))).((((....)))).)))...-)))))).)))..... ( -29.30)
>DroAna_CAF1 69140 115 - 1
CUUCUCCACUCCACACCCUCUGCCCAAUAACCGCCAAAGCACCUGGCAGUAUAUUAAAUACCGAAAAGUUCUCAGGUCGCUGAAGGGCAAGCGACCGAGGAAA-AUAUUUGGAAA---A
....((((........((((.....((((((.((((.......)))).)).))))...................(((((((........)))))))))))...-.....))))..---. ( -28.79)
>consensus
CUCCACCACUCCAC___________________CCCAAGUACUUUCGAGUAUAUUAAAUACCGGAAAGUUCUCAGGUCACUGAAGGGCAAACGUCCAUGGAAA_GUGGAAGGGAACAGG
.(((.((((((((....................((..((.((((((..((((.....))))..)))))).))..))........((((....)))).))))...))))...)))..... (-16.88 = -19.05 +   2.17)

alignment

secondary structure

dotplot

Window 2

Location	4,305,941 – 4,306,035
Length	94
Sequences	5
Columns	94
Reading direction	forward
Mean pairwise identity	92.66
Mean single sequence MFE	-29.96
Consensus MFE	-25.44
Energy contribution	-26.08
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-2.14
Structure conservation index	0.85
SVM decision value	2.29
SVM RNA-class probability	0.991877
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4305941 94 + 20766785
UGACCUGAGAACUUUCCGGUAUUUAAUAUACUCGAAAGUACUUGGGGUGGAGUGGUGGAGGCCAUUGGGCUGGCUGGUUCCUUGGUGAGAUGUG
...((..((.((((((.(((((.....))))).)))))).))..))..(((.((((...((((....)))).)))).))).............. ( -28.80)
>DroSec_CAF1 61151 94 + 1
UGACCUGAGAACUUUCCGGUAUUUAAUAUACUCGAAAGUACUUGGGGUGGAGUGGUGGAGGCCAUUGGGCUGGCUGGUUCAUUGGUGAGAUGUG
...((..((.((((((.(((((.....))))).)))))).))..))(((((.((((...((((....)))).)))).)))))............ ( -31.50)
>DroSim_CAF1 64547 94 + 1
UGACCGGAGAACUUUCCGGUAUUUAAUAUACUCGAAAGUACUUGGGGUGGAGUGGUGGAGGCCAUUGGGCUGGCUGGUUCAUUGGUGAGCUGUG
...((.(((.((((((.(((((.....))))).)))))).))).))....((((((....)))))).((((.((..(....)..)).))))... ( -32.20)
>DroEre_CAF1 60456 86 + 1
UGACCUGAGAACUUUCCGGCAUUUAAUAUACUCCAAAGUACUUGGGGU--------GGAGGCCAUUGGGCUGGGUGGUUCGUUGGUGAGAUGUG
(.(((...(((((.((((((........((((((((.....)))))))--------)...........)))))).)))))...))).)...... ( -28.41)
>DroYak_CAF1 61947 94 + 1
UGACCUGAGAACUUUCCGGUAUUUAAUAUACUCGAAAGUACUUGGGGUGGAAUGGUGGAGGCCAUUGGGCUGGGUGUUUCGUUGGUGAGAUGUG
...((..((.((((((.(((((.....))))).)))))).))..))((..((((((....))))))..))...(..(((((....)))))..). ( -28.90)
>consensus
UGACCUGAGAACUUUCCGGUAUUUAAUAUACUCGAAAGUACUUGGGGUGGAGUGGUGGAGGCCAUUGGGCUGGCUGGUUCAUUGGUGAGAUGUG
...((..((.((((((.(((((.....))))).)))))).))..))..............((((.((((((....)))))).))))........ (-25.44 = -26.08 +   0.64)

alignment

secondary structure

dotplot

Window 3

Location	4,305,941 – 4,306,035
Length	94
Sequences	5
Columns	94
Reading direction	reverse
Mean pairwise identity	92.66
Mean single sequence MFE	-16.70
Consensus MFE	-13.02
Energy contribution	-13.22
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.22
Structure conservation index	0.78
SVM decision value	1.22
SVM RNA-class probability	0.931844
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4305941 94 - 20766785
CACAUCUCACCAAGGAACCAGCCAGCCCAAUGGCCUCCACCACUCCACCCCAAGUACUUUCGAGUAUAUUAAAUACCGGAAAGUUCUCAGGUCA
.............(((....((((......)))).)))..........((..((.((((((..((((.....))))..)))))).))..))... ( -18.90)
>DroSec_CAF1 61151 94 - 1
CACAUCUCACCAAUGAACCAGCCAGCCCAAUGGCCUCCACCACUCCACCCCAAGUACUUUCGAGUAUAUUAAAUACCGGAAAGUUCUCAGGUCA
........(((...((((..((((......)))).......................(((((.((((.....))))))))).))))...))).. ( -17.00)
>DroSim_CAF1 64547 94 - 1
CACAGCUCACCAAUGAACCAGCCAGCCCAAUGGCCUCCACCACUCCACCCCAAGUACUUUCGAGUAUAUUAAAUACCGGAAAGUUCUCCGGUCA
....((((............((((......)))).......(((........)))......)))).........((((((......)))))).. ( -18.30)
>DroEre_CAF1 60456 86 - 1
CACAUCUCACCAACGAACCACCCAGCCCAAUGGCCUCC--------ACCCCAAGUACUUUGGAGUAUAUUAAAUGCCGGAAAGUUCUCAGGUCA
........(((...((((...((.((..((((..((((--------(............)))))..))))....)).))...))))...))).. ( -15.20)
>DroYak_CAF1 61947 94 - 1
CACAUCUCACCAACGAAACACCCAGCCCAAUGGCCUCCACCAUUCCACCCCAAGUACUUUCGAGUAUAUUAAAUACCGGAAAGUUCUCAGGUCA
..............((............(((((......)))))....((..((.((((((..((((.....))))..)))))).))..)))). ( -14.10)
>consensus
CACAUCUCACCAACGAACCAGCCAGCCCAAUGGCCUCCACCACUCCACCCCAAGUACUUUCGAGUAUAUUAAAUACCGGAAAGUUCUCAGGUCA
........(((...((((...((.(((....)))...................(((((....)))))..........))...))))...))).. (-13.02 = -13.22 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:05 2006