Locus 5501

Sequence ID	3R_DroMel_CAF1
Location	14,471,250 – 14,471,427
Length	177
Max. P	0.862363

overview

Window 2

Location	14,471,250 – 14,471,361
Length	111
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	77.44
Mean single sequence MFE	-34.20
Consensus MFE	-19.95
Energy contribution	-20.12
Covariance contribution	0.17
Combinations/Pair	1.38
Mean z-score	-1.91
Structure conservation index	0.58
SVM decision value	0.83
SVM RNA-class probability	0.862363
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14471250 111 + 27905053
CAGUUCCUCAGUUCCGCCGACUAUCGUGGUGGGCCAGAACUACAUUAUCCACCACAAAGAUAAGGAUCGAUACUAUCGCGCCCUGGUCAGCCAAAAGCUGACCAAUGAA---AA
.......(((.....(((((.((((((((((((..............))))))))...(((....)))))))...))).))..((((((((.....)))))))).))).---.. ( -33.54)
>DroSec_CAF1 8255 111 + 1
CAGCUCCUCUGUUCCGCCGACUAUCGUGGUGGGCCAGAACUACAUUAUCCGCCACAAAAAUCAGAAUCGAUUCUAUCGCGCCCUGGUCAGCCAAAAGCUGACCAAUGGA---AA
...........(((((((((.....((((((((..............)))))))).......((((....)))).))).))..((((((((.....))))))))..)))---). ( -34.24)
>DroSim_CAF1 1078 111 + 1
CAGCUCCUCUGUUCCGCCGACUAUCGUGGUAGGCCAGAACUACAUUAUCCGCCACAAAGAUCAGAAUCGAUUCUAUCGCGCCCUGGUUAGCCAAAAGCUGACCAACGGA---AA
.......((((..(..((.((....))))..)..)))).........((((.......(((.((((....)))))))......((((((((.....)))))))).))))---.. ( -29.20)
>DroEre_CAF1 17238 111 + 1
CAGCUGCUCCGUUCCGCCAGCUAUCGUGGUGGGUCAGCACUACAUUGUGCACCGCAAGGAUCAGGACCGAUUCUAUCGCGCCAUGGUCAGCCAAAAGCUGACCACUCGA---GG
.((((((........).))))).((((((((((((.((((......)))).((....)).....))))(((...))).)))))((((((((.....))))))))..)))---.. ( -43.60)
>DroYak_CAF1 1075 111 + 1
UGGCUUCUCUGUUCCGACGGAUAUCGUGGUGGGUCAGCACUACAUUAUCCACCACAAGGUUCAGGACCGAUUCUAUCGCGCCAUGGUCAGCCAAAAGCUAACCACUCGA---GA
.....((((.....(((..((.((((((((((((.(........).)))))))))..((((...)))))))))..))).....((((.(((.....))).))))...))---)) ( -33.80)
>DroPer_CAF1 1062 110 + 1
----UCCUCCAAGCCCACUACCAUUGUGGUGGGCCAGCACUACAUUGCCUACCAAGAGGGCCAGGAUUUCCUACACCGCGCCCUUGUCCGCCAGAAAGUGACGAAUAUACCCGA
----........(((((((((....)))))))))..(((((.....((..((...((((((((((....))).....).))))))))..)).....)))).)............ ( -30.80)
>consensus
CAGCUCCUCUGUUCCGCCGACUAUCGUGGUGGGCCAGAACUACAUUAUCCACCACAAAGAUCAGGAUCGAUUCUAUCGCGCCCUGGUCAGCCAAAAGCUGACCAAUGGA___AA
.........................((((((((..............))))))))............................((((((((.....)))))))).......... (-19.95 = -20.12 +   0.17)

alignment

secondary structure

dotplot

Window 3

Location	14,471,324 – 14,471,427
Length	103
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	75.06
Mean single sequence MFE	-28.09
Consensus MFE	-14.86
Energy contribution	-14.87
Covariance contribution	0.00
Combinations/Pair	1.29
Mean z-score	-1.86
Structure conservation index	0.53
SVM decision value	0.70
SVM RNA-class probability	0.828104
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14471324 103 - 27905053
AAAACUCACUCCGAACAACGAACAUGCAAAUGAACGCCUAUAUCCGUCAAAAAAACAUUGUACAAAUU---UUCAUUGGUCAGCUUUUGGCUGACCAGGGCGCGAU
..................((..(((....)))..(((((......(((((.......))).)).....---.....((((((((.....))))))))))))))).. ( -23.80)
>DroSec_CAF1 8329 103 - 1
AAAACUCACUCGGAACAAUGUACAUUCAAAUGAACGCCAAAAUCCGUCAGAAAAACAUUGUACAAAUU---UCCAUUGGUCAGCUUUUGGCUGACCAGGGCGCGAU
....(.(.(((((((...((((((......(((.((........))))).........))))))...)---)))..((((((((.....))))))))))).).).. ( -28.66)
>DroSim_CAF1 1152 103 - 1
AAAACUCACUCGGAACAAUGUACAUUCAAAUGAACGCCAAAAUCCGUCAGAAAAACAUUGUACAAAUU---UCCGUUGGUCAGCUUUUGGCUAACCAGGGCGCGAU
....(((...(((((...((((((......(((.((........))))).........))))))...)---)))).((((.(((.....))).)))))))...... ( -22.46)
>DroEre_CAF1 17312 103 - 1
AGAACUCACUCGCCACUGUGGACAUUAAGGUAGAGGCCCAUAUCCGGCAGGAAAACUUUGUAAACACC---UCGAGUGGUCAGCUUUUGGCUGACCAUGGCGCGAU
........(.((((...(((.....((((((....(((.......)))......))))))....))).---....(((((((((.....))))))))))))).).. ( -32.20)
>DroYak_CAF1 1149 103 - 1
AAAACUCACUCGCUUCUGUGAGCAUUAAAAUAAAUGCCCAUAUCCGGCAGAAAAACUUUCAACCAAUC---UCGAGUGGUUAGCUUUUGGCUGACCAUGGCGCGAU
.........((((...((((.(((((......))))).)))).((((..(((.....)))..))....---....(((((((((.....))))))))))).)))). ( -28.90)
>DroPer_CAF1 1132 106 - 1
UUCACUUACUCUCUGCUGUGCACAUUGAUAUUUAGGCCGAUGUCGGGCAGAAAGACAUCGUAGGUGUCGGGUAUAUUCGUCACUUUCUGGCGGACAAGGGCGCGGU
..............(((((((((.((((((((((...(((((((.........)))))))))))))))))))...(((((((.....))))))).....))))))) ( -32.50)
>consensus
AAAACUCACUCGCAACAAUGAACAUUCAAAUGAACGCCAAUAUCCGGCAGAAAAACAUUGUACAAAUC___UCCAUUGGUCAGCUUUUGGCUGACCAGGGCGCGAU
...................................(((....((.....))........................(((((((((.....))))))))))))..... (-14.86 = -14.87 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:56:48 2006