Locus 4008

Sequence ID	2R_DroMel_CAF1
Location	13,247,160 – 13,247,271
Length	111
Max. P	0.757634

overview

Window 8

Location	13,247,160 – 13,247,271
Length	111
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	77.24
Mean single sequence MFE	-34.42
Consensus MFE	-22.16
Energy contribution	-21.13
Covariance contribution	-1.02
Combinations/Pair	1.48
Mean z-score	-1.36
Structure conservation index	0.64
SVM decision value	0.29
SVM RNA-class probability	0.671056
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13247160 111 + 20766785
CACAUACGACGGCUCCUAAUUGGCAGUCGCUUGGUACUCCCUUUCAGACUAUAUCCGGACGCAGGCGUCCUUUGCCUGCAUAACACUGUUCGUGAUGAGCUUGGGUGCCGU
........(((((.((((...(((((((....((.....)).....)))).((((((((((((((((.....)))))))........))))).)))).))))))).))))) ( -39.80)
>DroVir_CAF1 6774 111 + 1
CUAUUGUUUCAGCUUUUAUUUGGUAGUGUUAUGGCACGCCAUUGCAGAUUACAUACGAACGCAGGCAUCGUUUGCCUGCAUCACAUUGUUCGUGAUGAGCCUGGGUGCUGU
.........((((.......((((.((((....))))))))...(((..(.((((((((((((((((.....)))))))........)))))).))))..)))...)))). ( -34.40)
>DroGri_CAF1 6695 111 + 1
CAUAUGUUUCCGUUUUUAUUUGGUAGUGGCGUGGUAUUUCCUUUCAGAUUAUAUUAGAACGCAGGCAUCCUUUGCCUGCAUUACGUUGUUUGUCAUGAGCCUGGGCGCUGU
.....((.((((..(((((.....((..(((((((.......(((.(((...))).))).(((((((.....))))))))))))))..))....)))))..)))).))... ( -27.90)
>DroWil_CAF1 5110 111 + 1
CGUGGUAGACAGCUUGUAAUGGGCAGUGACUUGGUAUACCCUUUCAGAUUACAUCCGCACGCAGGCAUCCUUUGCCUGCAUCACGCUAUUUGUCAUGAGUCUGGGAGCCGU
...(((...(((((..(.((.(((.((((...((....))....................(((((((.....))))))).)))))))....)).)..)).)))...))).. ( -31.20)
>DroAna_CAF1 5759 111 + 1
UUUAAGUAACAGCUCCUAAUUGGCAGUGGCUUGGUACUUCCUUUCAGACUAUAUCCGGACGCAGGCGUCCUUUGCCUGCAUUACGUUGUUCGUGAUGAGCUUGGGAGCUGU
........(((((((((((..(((((.((..((((.((.......))))))...))(((((....))))).)))))..(((((((.....)))))))...))))))))))) ( -42.10)
>DroPer_CAF1 5854 106 + 1
-----UUGACAGUCCGUAAUUGGCAGUGGGUUGGUAUUUCCUUUCAGACUACAUCCGAACGCAGGCAUCGUUUGCCUGCAUCACACUGUUCGUCAUGAGCCUGGGCGCCGU
-----......(((((.....((((((.((..((.....))..))..))).(((.((((((((((((.....)))))))........)))))..))).))))))))..... ( -31.10)
>consensus
CAUAUGUGACAGCUCCUAAUUGGCAGUGGCUUGGUACUCCCUUUCAGACUACAUCCGAACGCAGGCAUCCUUUGCCUGCAUCACACUGUUCGUCAUGAGCCUGGGAGCCGU
...........((.((((...(((.(((((..((....))....................(((((((.....)))))))............)))))..))))))).))... (-22.16 = -21.13 +  -1.02)

alignment

secondary structure

dotplot

Window 9

Location	13,247,160 – 13,247,271
Length	111
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	77.24
Mean single sequence MFE	-32.13
Consensus MFE	-17.08
Energy contribution	-17.22
Covariance contribution	0.14
Combinations/Pair	1.20
Mean z-score	-1.91
Structure conservation index	0.53
SVM decision value	0.49
SVM RNA-class probability	0.757634
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13247160 111 - 20766785
ACGGCACCCAAGCUCAUCACGAACAGUGUUAUGCAGGCAAAGGACGCCUGCGUCCGGAUAUAGUCUGAAAGGGAGUACCAAGCGACUGCCAAUUAGGAGCCGUCGUAUGUG
(((((.((...((....(((.....)))....)).((((..(((((....)))))((.(((..(((....))).))))).......)))).....)).)))))........ ( -35.10)
>DroVir_CAF1 6774 111 - 1
ACAGCACCCAGGCUCAUCACGAACAAUGUGAUGCAGGCAAACGAUGCCUGCGUUCGUAUGUAAUCUGCAAUGGCGUGCCAUAACACUACCAAAUAAAAGCUGAAACAAUAG
.((((...(((..((((.((((((........(((((((.....)))))))))))))))).)..)))..((((....)))).................))))......... ( -31.80)
>DroGri_CAF1 6695 111 - 1
ACAGCGCCCAGGCUCAUGACAAACAACGUAAUGCAGGCAAAGGAUGCCUGCGUUCUAAUAUAAUCUGAAAGGAAAUACCACGCCACUACCAAAUAAAAACGGAAACAUAUG
..........(((..............(.((((((((((.....)))))))))))........(((....)))........)))................(....)..... ( -24.50)
>DroWil_CAF1 5110 111 - 1
ACGGCUCCCAGACUCAUGACAAAUAGCGUGAUGCAGGCAAAGGAUGCCUGCGUGCGGAUGUAAUCUGAAAGGGUAUACCAAGUCACUGCCCAUUACAAGCUGUCUACCACG
((((((((((...(((((........)))))((((((((.....)))))))))).)))((((((......(((((...........))))))))))).)))))........ ( -32.10)
>DroAna_CAF1 5759 111 - 1
ACAGCUCCCAAGCUCAUCACGAACAACGUAAUGCAGGCAAAGGACGCCUGCGUCCGGAUAUAGUCUGAAAGGAAGUACCAAGCCACUGCCAAUUAGGAGCUGUUACUUAAA
((((((((......(((.(((.....))).)))..((((..(((((....)))))((.(((..(((....))).))))).......)))).....))))))))........ ( -36.20)
>DroPer_CAF1 5854 106 - 1
ACGGCGCCCAGGCUCAUGACGAACAGUGUGAUGCAGGCAAACGAUGCCUGCGUUCGGAUGUAGUCUGAAAGGAAAUACCAACCCACUGCCAAUUACGGACUGUCAA-----
..((.((....)))).(((((..(((((.((((((((((.....)))))))))).((.(((..(((....))).)))))....)))))((......))..))))).----- ( -33.10)
>consensus
ACAGCACCCAGGCUCAUCACGAACAACGUGAUGCAGGCAAAGGAUGCCUGCGUUCGGAUAUAAUCUGAAAGGAAAUACCAAGCCACUGCCAAUUAAAAGCUGUCACAUAAG
.((((.........................((((((((.......))))))))..........(((....))).........................))))......... (-17.08 = -17.22 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:34 2006