Locus 8565

Sequence ID	3R_DroMel_CAF1
Location	22,881,727 – 22,881,912
Length	185
Max. P	0.926515

overview

Window 1

Location	22,881,727 – 22,881,838
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	88.87
Mean single sequence MFE	-32.35
Consensus MFE	-24.56
Energy contribution	-26.38
Covariance contribution	1.81
Combinations/Pair	1.03
Mean z-score	-2.50
Structure conservation index	0.76
SVM decision value	1.18
SVM RNA-class probability	0.926515
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22881727 111 + 27905053
AUUUUAGAUGUGCAAACUGAA---------UGUAUCAUGCCUUUGUUUCAGGCCGUUAAACUUUAUGUCUAGUUUUUUAUUCAGGUGGUCACGUUAAAGAGACGUGGCCACUGAGUUCAU
.......(((.((...(((((---------((......((((.......))))....(((((........)))))..)))))))(((((((((((.....)))))))))))...)).))) ( -31.70)
>DroSec_CAF1 26725 120 + 1
ACUUUAGAUGUGCAAACUGAACUUAAGAUCUUUAUCAAGCCUUUGUUUCAGGCCGUAAAACUUUAUGUCUAGUUUUUUAUUCAGGUGGUCACGUUAAAGAGACGUGGCCACUGAGUUCAU
.................(((((((..((..........((((.......))))...((((((........))))))....)).((((((((((((.....))))))))))))))))))). ( -32.30)
>DroSim_CAF1 27905 119 + 1
ACUUUAGAUGUGAAAACUGAACUUAA-AUCUUUAUCAUGCCUUUGUUUCAGGCCGUAAAACUUUAUGUCUAGUUUUUUAUUCAGGUAGUCACGUUAAAGAGACGUGGCCACUGAGUUCAU
...........((((((((.((.(((-(..(((((...((((.......)))).)))))..)))).)).)))))))).((((((...((((((((.....))))))))..)))))).... ( -29.70)
>DroYak_CAF1 31364 120 + 1
ACUCCAGAUGUGUAAGCUGAACUAAACAUCUCAAUCGUGGCUUUGUUUCAUGCCGUAAAACUUUAUGUCUAGUUUUUUAUUUAGGUGGUCACGUUAAAGAGACGUGGCCACCGAGUUCAU
((((....((.(((((..((((((.((((.....(..((((..........))))..)......)))).))))))))))).))((((((((((((.....)))))))))))))))).... ( -35.70)
>consensus
ACUUUAGAUGUGCAAACUGAACUUAA_AUCUUUAUCAUGCCUUUGUUUCAGGCCGUAAAACUUUAUGUCUAGUUUUUUAUUCAGGUGGUCACGUUAAAGAGACGUGGCCACUGAGUUCAU
.................(((((((..............((((.......))))...((((((........)))))).......((((((((((((.....))))))))))))))))))). (-24.56 = -26.38 +   1.81)

alignment

secondary structure

dotplot

Window 2

Location	22,881,727 – 22,881,838
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.87
Mean single sequence MFE	-27.75
Consensus MFE	-20.66
Energy contribution	-21.35
Covariance contribution	0.69
Combinations/Pair	1.10
Mean z-score	-2.45
Structure conservation index	0.74
SVM decision value	1.02
SVM RNA-class probability	0.901996
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22881727 111 - 27905053
AUGAACUCAGUGGCCACGUCUCUUUAACGUGACCACCUGAAUAAAAAACUAGACAUAAAGUUUAACGGCCUGAAACAAAGGCAUGAUACA---------UUCAGUUUGCACAUCUAAAAU
.........((((.(((((.......))))).))))((((((.......(((((.....)))))...((((.......)))).......)---------)))))................ ( -24.50)
>DroSec_CAF1 26725 120 - 1
AUGAACUCAGUGGCCACGUCUCUUUAACGUGACCACCUGAAUAAAAAACUAGACAUAAAGUUUUACGGCCUGAAACAAAGGCUUGAUAAAGAUCUUAAGUUCAGUUUGCACAUCUAAAGU
......(((((((.(((((.......))))).))).)))).....(((((..((.(((..((((..(((((.......))))).....))))..))).))..)))))............. ( -27.40)
>DroSim_CAF1 27905 119 - 1
AUGAACUCAGUGGCCACGUCUCUUUAACGUGACUACCUGAAUAAAAAACUAGACAUAAAGUUUUACGGCCUGAAACAAAGGCAUGAUAAAGAU-UUAAGUUCAGUUUUCACAUCUAAAGU
......(((((((.(((((.......))))).))).))))....((((((..((.((((.(((((((((((.......)))).)).))))).)-))).))..))))))............ ( -26.80)
>DroYak_CAF1 31364 120 - 1
AUGAACUCGGUGGCCACGUCUCUUUAACGUGACCACCUAAAUAAAAAACUAGACAUAAAGUUUUACGGCAUGAAACAAAGCCACGAUUGAGAUGUUUAGUUCAGCUUACACAUCUGGAGU
....(((((((((.(((((.......))))).))))).........((((((((((..((((....(((..........)))..))))...))))))))))...............)))) ( -32.30)
>consensus
AUGAACUCAGUGGCCACGUCUCUUUAACGUGACCACCUGAAUAAAAAACUAGACAUAAAGUUUUACGGCCUGAAACAAAGGCAUGAUAAAGAU_UUAAGUUCAGUUUGCACAUCUAAAGU
.((((((((((((.(((((.......))))).))).))))....((((((........)))))).((((((.......)))).)).............)))))................. (-20.66 = -21.35 +   0.69)

alignment

secondary structure

dotplot

Window 3

Location	22,881,798 – 22,881,912
Length	114
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	84.44
Mean single sequence MFE	-28.21
Consensus MFE	-22.46
Energy contribution	-23.40
Covariance contribution	0.94
Combinations/Pair	1.06
Mean z-score	-1.43
Structure conservation index	0.80
SVM decision value	-0.02
SVM RNA-class probability	0.524381
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22881798 114 + 27905053
UCAGGUGGUCACGUUAAAGAGACGUGGCCACUGAGUUCAUCGUUAAAGUAAACUAAGCCACCAUAUUCGCAAUU------CAGGUCGAUUGUAUUUGCUUGCAGAAAAACAAUCCAAACU
((((.((((((((((.....))))))))))))))(((..((....(((((((.....(.(((............------..))).)......)))))))...))..))).......... ( -28.34)
>DroSec_CAF1 26805 120 + 1
UCAGGUGGUCACGUUAAAGAGACGUGGCCACUGAGUUCAUCGUUAAAGUAAACUAAGCCACCAUAUUCGCAAUUCGGUUUCAGGUCGAUUGUAUCUGCUUGCAGAAAAACAAUCCAAACC
((((.((((((((((.....)))))))))))))).......(((........(((((((................))))).))...((((((.((((....))))...))))))..))). ( -32.19)
>DroSim_CAF1 27984 120 + 1
UCAGGUAGUCACGUUAAAGAGACGUGGCCACUGAGUUCAUCGUUAAAGUAAACUAAGCCACCAUAUUCGCAAUUCGGUUUCAGGUCGAUUGUAUCUGCUUGCAGAAAAACAAUGCAAACU
((((...((((((((.....))))))))..))))((((((.(((........................(((((.(((.......)))))))).((((....))))..))).)))..))). ( -25.20)
>DroYak_CAF1 31444 103 + 1
UUAGGUGGUCACGUUAAAGAGACGUGGCCACCGAGUUCAUUGUUAAAGUAAACUAAGCCACCAUAUUCUUAAAUCAGUUUCUGGUCGAUU---------U--------GCAAUCAAAAUU
...((((((((((((.....))))))))))))...............(((((.....(.((((.(..((......))..).)))).).))---------)--------)).......... ( -27.10)
>consensus
UCAGGUGGUCACGUUAAAGAGACGUGGCCACUGAGUUCAUCGUUAAAGUAAACUAAGCCACCAUAUUCGCAAUUCGGUUUCAGGUCGAUUGUAUCUGCUUGCAGAAAAACAAUCCAAACU
...((((((((((((.....))))))))))))((((.....(((..((....)).)))......))))..................((((((.((((....))))...))))))...... (-22.46 = -23.40 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:14:15 2006