Locus 5152

Sequence ID	2L_DroMel_CAF1
Location	14,602,757 – 14,602,877
Length	120
Max. P	0.962600

overview

Window 6

Location	14,602,757 – 14,602,877
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.50
Mean single sequence MFE	-46.92
Consensus MFE	-25.24
Energy contribution	-25.85
Covariance contribution	0.61
Combinations/Pair	1.30
Mean z-score	-2.78
Structure conservation index	0.54
SVM decision value	1.34
SVM RNA-class probability	0.944423
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14602757 120 + 22407834
UUCCUAAUUCCUCGCUCAGCUCCUGACGCUGCUGCAGGAGCAGUUCCUGCUCCUGCUCCUGGCUGGCGCACUUUUCCAGUGCUUGGGCCAGGUCAGUCUCCCGCUGCUCCAGCAGCUGCU
................(((((.(((..((.((.((((((((((...)))))))))).(((((((.(.(((((.....))))).).)))))))..........)).))..))).))))).. ( -54.60)
>DroVir_CAF1 1428 120 + 1
GGCCCAGCUCGUCGCUUAGCUCGUCGCGCUGCUUCAACAGCUUCUGCUGCUCCUGCUCUUGGCUGGCGCACUUCUCCAGUGCGAUCGCCAGUUCGUUUUCACGCUGCUCCAACAGCUGUU
((..((((.((.((.......)).)).))))..))(((((((..((..((....((..(((((...((((((.....))))))...)))))...((....)))).))..))..))))))) ( -37.00)
>DroGri_CAF1 7588 120 + 1
GUCCCAGCUCGUCGCUCAGCUCGUGGCGCUGUUGGAGCAGCUGUUGUUGCUCCUGUUCCUGGUUGGCACACUUCUCCAGCGCCAGGGCCAAUUCGCUCUCGCGCUGUUCGAGCAGCUGUU
....(((((..(((..((((.((((((((((..((((((((....))))))))(((.((.....)).)))......))))))))((((......)))).)).))))..)))..))))).. ( -55.00)
>DroYak_CAF1 11345 120 + 1
UUCCCAGUUCCUCACUCAGCUCGCGACGCUGCUGCAGGAGCAGCUCCUGUUCCUGCUCCUGGCUGGCACACUUUUCCAGAGCUUGGGCCAGGUCACUUUCCCGCUGCUCCAGCAGCUGCU
.(((.((((........)))).).)).((.(((((.((((((((.((((..((.((((.(((..((....))...)))))))..))..))))..........)))))))).))))).)). ( -47.00)
>DroMoj_CAF1 7652 120 + 1
GGCCCAGUUCGUCGCUUAGUUCAUUGCGCUGCUUCAGCAGCAGCUGCUGCUCCUGCUCCUGGCUGACGCACUUCUCCAGGGCGGCUGCCAAUUCGCUCUCACGCUGCUCCAGCAGCUGCU
(((.......)))............((((((((..((((((((((((.((....)).(((((..((......)).)))))))))))((......))......))))))..)))))).)). ( -43.20)
>DroAna_CAF1 1971 120 + 1
GACUCAACUCCUCGCUCAGCUCCUGCCGCUGUUGCAGCAGCAGCUCUUGCUCCUGCUCCUGGCUGGCGCAUUUUUCGAGGGCCUGAGCCAGCUCGCUUUCCCGCUGCUCCAGCAGCUGCU
(.((((..((((((....((.((.(((((....))(((((.(((....))).)))))...))).)).))......))))))..)))).).............(((((....))))).... ( -44.70)
>consensus
GUCCCAGCUCCUCGCUCAGCUCGUGGCGCUGCUGCAGCAGCAGCUCCUGCUCCUGCUCCUGGCUGGCGCACUUCUCCAGGGCCUGGGCCAGUUCGCUCUCCCGCUGCUCCAGCAGCUGCU
...........................((((((..((((((.......((....))..(((((.(((.(.........).)))...)))))...........))))))..)))))).... (-25.24 = -25.85 +   0.61)

alignment

secondary structure

dotplot

Window 7

Location	14,602,757 – 14,602,877
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.50
Mean single sequence MFE	-51.37
Consensus MFE	-28.04
Energy contribution	-28.43
Covariance contribution	0.39
Combinations/Pair	1.39
Mean z-score	-2.94
Structure conservation index	0.55
SVM decision value	1.54
SVM RNA-class probability	0.962600
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14602757 120 - 22407834
AGCAGCUGCUGGAGCAGCGGGAGACUGACCUGGCCCAAGCACUGGAAAAGUGCGCCAGCCAGGAGCAGGAGCAGGAACUGCUCCUGCAGCAGCGUCAGGAGCUGAGCGAGGAAUUAGGAA
..(((((.(((..((.((((....))..((((((....(((((.....)))))....)))))).((((((((((...)))))))))).)).))..))).)))))................ ( -61.90)
>DroVir_CAF1 1428 120 - 1
AACAGCUGUUGGAGCAGCGUGAAAACGAACUGGCGAUCGCACUGGAGAAGUGCGCCAGCCAAGAGCAGGAGCAGCAGAAGCUGUUGAAGCAGCGCGACGAGCUAAGCGACGAGCUGGGCC
..(((((((((.(((.(((((.........((((...((((((.....))))))...))))...((...((((((....))))))...))..)))).)..)))...)))).))))).... ( -45.00)
>DroGri_CAF1 7588 120 - 1
AACAGCUGCUCGAACAGCGCGAGAGCGAAUUGGCCCUGGCGCUGGAGAAGUGUGCCAACCAGGAACAGGAGCAACAACAGCUGCUCCAACAGCGCCACGAGCUGAGCGACGAGCUGGGAC
..(((((..(((..((((((....))........(.((((((((......(((.((.....)).)))((((((........))))))..)))))))).).))))..)))..))))).... ( -52.00)
>DroYak_CAF1 11345 120 - 1
AGCAGCUGCUGGAGCAGCGGGAAAGUGACCUGGCCCAAGCUCUGGAAAAGUGUGCCAGCCAGGAGCAGGAACAGGAGCUGCUCCUGCAGCAGCGUCGCGAGCUGAGUGAGGAACUGGGAA
.((.(((((.(((((((((((..((....))..)))..(((((((....(....)...))).))))..........)))))))).))))).))........((.(((.....))).)).. ( -49.70)
>DroMoj_CAF1 7652 120 - 1
AGCAGCUGCUGGAGCAGCGUGAGAGCGAAUUGGCAGCCGCCCUGGAGAAGUGCGUCAGCCAGGAGCAGGAGCAGCAGCUGCUGCUGAAGCAGCGCAAUGAACUAAGCGACGAACUGGGCC
(((((((((((..((..(((....))).....))..(((((((((.((......))..))))).)).))..)))))))))))(((..((..((((..........))).)...)).))). ( -45.80)
>DroAna_CAF1 1971 120 - 1
AGCAGCUGCUGGAGCAGCGGGAAAGCGAGCUGGCUCAGGCCCUCGAAAAAUGCGCCAGCCAGGAGCAGGAGCAAGAGCUGCUGCUGCAACAGCGGCAGGAGCUGAGCGAGGAGUUGAGUC
(((.(((((....)))))(......)..)))(((((((..(((((.....(((.((.((.....)).)).)))..((((.(((((((....))))))).))))...)))))..))))))) ( -53.80)
>consensus
AGCAGCUGCUGGAGCAGCGGGAAAGCGAACUGGCCCAAGCACUGGAAAAGUGCGCCAGCCAGGAGCAGGAGCAGCAGCUGCUGCUGCAGCAGCGCCACGAGCUGAGCGACGAACUGGGAC
....((((((..((((((((....))...(((((....((.((.....)).))....))))).................))))))..))))))........((.(((.....))).)).. (-28.04 = -28.43 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:21 2006