Locus 5571

Sequence ID	3L_DroMel_CAF1
Location	15,267,218 – 15,267,378
Length	160
Max. P	0.705339

overview

Window 1

Location	15,267,218 – 15,267,338
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	90.72
Mean single sequence MFE	-38.03
Consensus MFE	-32.94
Energy contribution	-33.08
Covariance contribution	0.14
Combinations/Pair	1.17
Mean z-score	-1.60
Structure conservation index	0.87
SVM decision value	0.36
SVM RNA-class probability	0.705339
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15267218 120 - 23771897
UUCCAAAGCACCCAAAGUAUUGGAUGCCCAUUGUCUGGGCCGCCAGUAUUGUAACAAGGGCUCGAAAGGAAGGUCGAAUUUGGGAUGACUUCUCCCUGAAGUCCAUGAUAGAUGAGCUCA
......(((.(((((((((((((..(((((.....)))))..))))))))........(((((....)...))))....)))))..((((((.....))))))............))).. ( -37.70)
>DroSec_CAF1 2811 120 - 1
UUCCAAAGCACCCUAAGUACUGGAUGCCCAUCGUCUGGGCCGCCAGUAUUGUAACAAGAGCUCGAAAGGAAGGUCGAAUCUGGGAUGACUUCUCACUGAAGUCCAUGAUAGAUGAGCUCA
...............((((((((..(((((.....)))))..)))))))).......((((((((........))..(((((..((((((((.....))))).)))..))))))))))). ( -41.80)
>DroSim_CAF1 2666 120 - 1
UUCCAAAGCACCCUAAGUACUGGAUGCCCAUCGUUUGGGCCGCCAGUAUUGUAACAAGGGCUCGAAAGGAAGGUCGAAUCUGGGAUGAUUUCUCACUUAAGUCCAUGAUAGAUGAGCUCA
...............((((((((..(((((.....)))))..)))))))).......(((((((.......((.(.....(((((.....))))).....).))........))))))). ( -36.26)
>DroEre_CAF1 2839 120 - 1
UUCCAAAGCACCCCAAGUACUGGAUGCCCCUCGUUUGGGCCGCCAGUAUUGUAACAAGGGCUCGGAAGGAAGGUAGAAUAUGGGAUGACUUCUCACUGAAGUCCAUGAUCGAUGAGCUCA
...............((((((((..((((.......))))..)))))))).......(((((((...........((.(((((....(((((.....)))))))))).))..))))))). ( -36.02)
>DroYak_CAF1 2833 120 - 1
UUCCAAAGCACCCUAAGUACUGGAUGCCCAUCGUUUGGGCGGCCAGUAUUGUAACAAGGGCUCGGAAGGAAGGUAGAAUAUGGGAUGACUUCUCACUGAAGUCCAUGAUUGAUGAGCUCA
......(((......((((((((.((((((.....)))))).))))))))....((.((((((((..(((((................)))))..))).))))).))........))).. ( -39.39)
>DroAna_CAF1 3754 120 - 1
UUCCCAAGCAUCCAAAGUACUGGAUGCCCAUUAUUUGGGCCAGCAGUAUUGUGACGAGAGCUCGAAAGGAGGGACGCAUUUGGGACGAUUUCUCACUGAAGUCCAUGAUUGAUGAGCUUA
.((((((((.(((..(((((((...(((((.....)))))...)))))))....(((....))).......))).))..)))))).((((((.....))))))................. ( -37.00)
>consensus
UUCCAAAGCACCCUAAGUACUGGAUGCCCAUCGUUUGGGCCGCCAGUAUUGUAACAAGGGCUCGAAAGGAAGGUCGAAUAUGGGAUGACUUCUCACUGAAGUCCAUGAUAGAUGAGCUCA
...............((((((((..(((((.....)))))..)))))))).......(((((((........(((........)))((((((.....)))))).........))))))). (-32.94 = -33.08 +   0.14)

alignment

secondary structure

dotplot

Window 2

Location	15,267,258 – 15,267,378
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	89.06
Mean single sequence MFE	-33.00
Consensus MFE	-28.44
Energy contribution	-29.22
Covariance contribution	0.78
Combinations/Pair	1.10
Mean z-score	-1.59
Structure conservation index	0.86
SVM decision value	0.22
SVM RNA-class probability	0.640653
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15267258 120 + 23771897
AAUUCGACCUUCCUUUCGAGCCCUUGUUACAAUACUGGCGGCCCAGACAAUGGGCAUCCAAUACUUUGGGUGCUUUGGAAACUUCACAUCCAUUGCCUUCAUAAUAUUUGCCUCGUUGGC
...........((...(((((...(((((.....((((....)))).((((((((((((((....))))))))...(....).......))))))......)))))...).))))..)). ( -31.50)
>DroSec_CAF1 2851 120 + 1
GAUUCGACCUUCCUUUCGAGCUCUUGUUACAAUACUGGCGGCCCAGACGAUGGGCAUCCAGUACUUAGGGUGCUUUGGAAACUUCACAUCCAUUGCCUUCAUAAUAUUUGCCUCGUUGGC
...........((...(((((...(((((...((((((..(((((.....)))))..))))))....(((((....(....)....)))))..........)))))...).))))..)). ( -34.50)
>DroSim_CAF1 2706 120 + 1
GAUUCGACCUUCCUUUCGAGCCCUUGUUACAAUACUGGCGGCCCAAACGAUGGGCAUCCAGUACUUAGGGUGCUUUGGAAACUUUACAUCCAUUGCCUUCAUAAUAUUUGCCUCGUUGGC
...((((........))))(((((........((((((..(((((.....)))))..))))))...)))))((..((((.........))))..)).............(((.....))) ( -33.70)
>DroEre_CAF1 2879 120 + 1
UAUUCUACCUUCCUUCCGAGCCCUUGUUACAAUACUGGCGGCCCAAACGAGGGGCAUCCAGUACUUGGGGUGCUUUGGAAACUUGACAUCCAUUGCCUUCAUUAUGUUUGCCUCGUUGGC
...................(((((.((......)).)).)))((((....((((((..((.....(((((.((..((((.........))))..)))))))...))..)))))).)))). ( -33.50)
>DroYak_CAF1 2873 120 + 1
UAUUCUACCUUCCUUCCGAGCCCUUGUUACAAUACUGGCCGCCCAAACGAUGGGCAUCCAGUACUUAGGGUGCUUUGGAAACUUGACAUCCAUUGCCUUCAUAAUAUUUGCCUCAUUGGC
.............(((((((((((((......((((((..(((((.....)))))..))))))..))))).)).)))))).............................(((.....))) ( -32.30)
>DroAna_CAF1 3794 120 + 1
AAUGCGUCCCUCCUUUCGAGCUCUCGUCACAAUACUGCUGGCCCAAAUAAUGGGCAUCCAGUACUUUGGAUGCUUGGGAAACUUGACGUCCAUACCUCUGAUUAUAUUGGCCUCGUUGGU
...........((...((((((...((((...(((((...(((((.....)))))...)))))...((((((...((....))...))))))......))))......)).))))..)). ( -32.50)
>consensus
AAUUCGACCUUCCUUUCGAGCCCUUGUUACAAUACUGGCGGCCCAAACGAUGGGCAUCCAGUACUUAGGGUGCUUUGGAAACUUGACAUCCAUUGCCUUCAUAAUAUUUGCCUCGUUGGC
...........((...(((((...(((((...((((((..(((((.....)))))..))))))....(((((....(....)....)))))..........)))))...).))))..)). (-28.44 = -29.22 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:41 2006