Locus 2172

Sequence ID	3R_DroMel_CAF1
Location	6,231,759 – 6,231,868
Length	109
Max. P	0.825927

overview

Window 5

Location	6,231,759 – 6,231,868
Length	109
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	81.11
Mean single sequence MFE	-29.17
Consensus MFE	-21.85
Energy contribution	-22.02
Covariance contribution	0.17
Combinations/Pair	1.19
Mean z-score	-1.83
Structure conservation index	0.75
SVM decision value	0.70
SVM RNA-class probability	0.825927
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6231759 109 + 27905053
CAUGAUCGUCAAAGAGGCGACGCGAGAAAAAGUGGCGCAGCCUCUUGUGCGGUUGGAAAAGCCAGAAGUACAGACUUUG-GAGAAAAUUAUUAUUAACCUUAUGA---UAGGA
.......(((.(((((((..(((.(.......).)))..)))))))((((..((((.....))))..)))).)))....-.................(((.....---.))). ( -31.30)
>DroGri_CAF1 2361 108 + 1
CAUGAUCAUCAAACAGACGACGCGAGAAAAAGUAACGUAGUUUUUUGUGCGGUUGAAACAGCCAAAAGUAAAGCCUGU-AAAGUAGAGAUUGAUUAAC----UGCCUAUUUGG
..((((((((..((((.(.(((((.((((((.((...)).)))))).)))(((((...)))))....))...).))))-........)).))))))..----........... ( -16.60)
>DroSec_CAF1 4846 109 + 1
CAUGAUCAUCAAAGAGGCGACGCGAGAAAAAGUGGCGUAGCCUCUUGUGCGGUUGGAACAGCCAGAAGUACAGACUUCG-GAGAAGAUUAUGAUUAACCUUAUGA---UGGGA
(((((((.((.(((((((.((((.(.......).)))).)))))))((((..((((.....))))..))))...(....-).)).))))))).....(((.....---.))). ( -37.70)
>DroSim_CAF1 7084 109 + 1
CAUGAUCGUCAAAGAGGCGACGCGAGAAAAAGUGGCGUAGCCUCUUGUGCGGUUGGAACAGCCAGAAGUACAGACUUUG-GAGAAAAUUAUGAUUAACCAUAUGA---UGGGA
((((((..((.(((((((.((((.(.......).)))).)))))))((((..((((.....))))..))))........-..))..)))))).....((((...)---))).. ( -34.60)
>DroEre_CAF1 4888 103 + 1
UAUGAUCGUCAAAGAGGCGACGCGAGAAGAAGUGGCGCAGCCUCUUGUGUGGUUGGAACAGCCAGAAGUACAGACUUUG-GGGAACGUUAUGAUAAG------GA---UAUAA
.(((.((.((((((((((..(((.(.......).)))..)))))(((((((((((...))))))....)))))..))))-).)).))).........------..---..... ( -26.80)
>DroYak_CAF1 4977 103 + 1
UAUGAUCGUCAAAGAGGCGACGCGAGAAGAAGUGGCGCAGCCUCUUGUGUGGUUGGAACAGCCAGAGGUACAGACUUUG-GGGAGAGAUAUGAUUAA------UA---UAGGA
..(((((((..(((((((..(((.(.......).)))..)))))))...............((((((.......)))))-)........))))))).------..---..... ( -28.00)
>consensus
CAUGAUCGUCAAAGAGGCGACGCGAGAAAAAGUGGCGCAGCCUCUUGUGCGGUUGGAACAGCCAGAAGUACAGACUUUG_GAGAAAAUUAUGAUUAAC____UGA___UAGGA
..(((((((..(((((((..(((.(.......).)))..)))))))((((..((((.....))))..))))..................)))))))................. (-21.85 = -22.02 +   0.17)

alignment

secondary structure

dotplot

Window 6

Location	6,231,759 – 6,231,868
Length	109
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	81.11
Mean single sequence MFE	-21.77
Consensus MFE	-15.94
Energy contribution	-15.42
Covariance contribution	-0.52
Combinations/Pair	1.29
Mean z-score	-1.54
Structure conservation index	0.73
SVM decision value	0.39
SVM RNA-class probability	0.717359
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6231759 109 - 27905053
UCCUA---UCAUAAGGUUAAUAAUAAUUUUCUC-CAAAGUCUGUACUUCUGGCUUUUCCAACCGCACAAGAGGCUGCGCCACUUUUUCUCGCGUCGCCUCUUUGACGAUCAUG
.(((.---.....))).................-.((((((.........))))))......((((.(((((((.((((...........)))).))))))))).))...... ( -22.90)
>DroGri_CAF1 2361 108 - 1
CCAAAUAGGCA----GUUAAUCAAUCUCUACUUU-ACAGGCUUUACUUUUGGCUGUUUCAACCGCACAAAAAACUACGUUACUUUUUCUCGCGUCGUCUGUUUGAUGAUCAUG
.(((((((((.----...................-((((.(.........).))))......(((...(((((.........)))))...)))..)))))))))......... ( -16.50)
>DroSec_CAF1 4846 109 - 1
UCCCA---UCAUAAGGUUAAUCAUAAUCUUCUC-CGAAGUCUGUACUUCUGGCUGUUCCAACCGCACAAGAGGCUACGCCACUUUUUCUCGCGUCGCCUCUUUGAUGAUCAUG
...((---(((...((((...............-.(((((....))))).((.....))))))....(((((((.((((...........)))).))))))))))))...... ( -27.70)
>DroSim_CAF1 7084 109 - 1
UCCCA---UCAUAUGGUUAAUCAUAAUUUUCUC-CAAAGUCUGUACUUCUGGCUGUUCCAACCGCACAAGAGGCUACGCCACUUUUUCUCGCGUCGCCUCUUUGACGAUCAUG
.....---...(((((((..............(-((((((....)))).)))...........(((.(((((((.((((...........)))).))))))))).)))))))) ( -22.90)
>DroEre_CAF1 4888 103 - 1
UUAUA---UC------CUUAUCAUAACGUUCCC-CAAAGUCUGUACUUCUGGCUGUUCCAACCACACAAGAGGCUGCGCCACUUCUUCUCGCGUCGCCUCUUUGACGAUCAUA
.....---..------..........((((..(-((((((....)))).)))...............(((((((.((((...........)))).))))))).))))...... ( -21.10)
>DroYak_CAF1 4977 103 - 1
UCCUA---UA------UUAAUCAUAUCUCUCCC-CAAAGUCUGUACCUCUGGCUGUUCCAACCACACAAGAGGCUGCGCCACUUCUUCUCGCGUCGCCUCUUUGACGAUCAUA
.....---..------.................-....(((........(((.((...)).)))...(((((((.((((...........)))).))))))).)))....... ( -19.50)
>consensus
UCCUA___UCA____GUUAAUCAUAAUUUUCUC_CAAAGUCUGUACUUCUGGCUGUUCCAACCGCACAAGAGGCUACGCCACUUUUUCUCGCGUCGCCUCUUUGACGAUCAUG
......................................(((........(((.....))).......(((((((.((((...........)))).))))))).)))....... (-15.94 = -15.42 +  -0.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:05 2006