Locus 5105

Sequence ID	3R_DroMel_CAF1
Location	13,448,252 – 13,448,354
Length	102
Max. P	0.792715

overview

Window 5

Location	13,448,252 – 13,448,354
Length	102
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	86.89
Mean single sequence MFE	-37.90
Consensus MFE	-33.07
Energy contribution	-33.07
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.49
Structure conservation index	0.87
SVM decision value	0.13
SVM RNA-class probability	0.599936
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13448252 102 + 27905053
AGC-G------GCGCUCACAUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGAAGGUUUA-UUUU---U
(((-(------((((((.((((.(((......))).))))...)))))).)))).....(.((.(((((.(((((.......))))).))))))).).......-....---. ( -40.40)
>DroSim_CAF1 3490 101 + 1
AAU-G------GCGCUCACAUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGAGUGAUUA-UUUU----
...-.------((((((.((((.(((......))).))))...))))))((((((......((.(((((.(((((.......))))).)))))))))))))...-....---- ( -38.10)
>DroEre_CAF1 1547 101 + 1
AGC-G------CCGCUCACAUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGAAGGAUUU-UUUU----
(((-(------.(((((.((((.(((......))).))))...)))))..)))).....(.((.(((((.(((((.......))))).))))))).).......-....---- ( -35.30)
>DroWil_CAF1 7605 112 + 1
AUUGGGCGCGAGCUAACACAUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGUUGGAAGU-UUCUUUUU
...((((((...(((...((((.(((......))).)))).))).))))))((((..((..((.(((((.(((((.......))))).)))))))..)).))))-........ ( -40.40)
>DroYak_CAF1 4200 101 + 1
GUG-G------CCGCCCACAUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGAAGGGUUA-UUUU----
...-.------..((((...((((((((((..((((.(((.(.((((....))))).))).))))......((((.......)))))))))))).)).))))..-....---- ( -37.70)
>DroAna_CAF1 4191 100 + 1
AGC-G------GCGCCCUCAUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUACCCCGCAUCUCCAAG-UAUUUAAUUU-----
(((-(------((((.((((((.(((......))).))))..)).)))).))))..((...((.(((((.(((((.......))))).))))))).)-).........----- ( -35.50)
>consensus
AGC_G______GCGCUCACAUCGGGGAUGUAGCUCAGAUGGUAGAGCGCUCGCUUAGCAUGUGAGAGGUACGGGGAUCGAUGCCCCGCAUCUCCAGAAGGAUUA_UUUU____
......................((((((((..((((.(((.(.((((....))))).))).))))......((((.......))))))))))))................... (-33.07 = -33.07 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	13,448,252 – 13,448,354
Length	102
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	86.89
Mean single sequence MFE	-34.30
Consensus MFE	-27.73
Energy contribution	-27.90
Covariance contribution	0.17
Combinations/Pair	1.04
Mean z-score	-2.39
Structure conservation index	0.81
SVM decision value	0.59
SVM RNA-class probability	0.792715
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13448252 102 - 27905053
A---AAAA-UAAACCUUCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAUGUGAGCGC------C-GCU
.---....-..........((((.(((((((.......))))))).)))).........((((.((((((...((((.((......))...)))).))))))------)-))) ( -35.60)
>DroSim_CAF1 3490 101 - 1
----AAAA-UAAUCACUCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAUGUGAGCGC------C-AUU
----....-.........(((((.(((((((.......))))))).))((((((((((.....)))((((........))))..........)))))))..)------)-).. ( -30.20)
>DroEre_CAF1 1547 101 - 1
----AAAA-AAAUCCUUCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAUGUGAGCGG------C-GCU
----....-...(((....)))..(((((((.......)))))))((.((((((((((.....)))((((........))))..........))))))).))------.-... ( -33.60)
>DroWil_CAF1 7605 112 - 1
AAAAAGAA-ACUUCCAACUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAUGUGUUAGCUCGCGCCCAAU
........-..........((((.(((((((.......))))))).))))..........((((((((((........))))((((((...))))))...))))))....... ( -37.70)
>DroYak_CAF1 4200 101 - 1
----AAAA-UAACCCUUCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAUGUGGGCGG------C-CAC
----....-.........(((...(((((((.......)))))))((.((((((((((.....)))((((........))))..........))))))).))------)-)). ( -32.20)
>DroAna_CAF1 4191 100 - 1
-----AAAUUAAAUA-CUUGGAGAUGCGGGGUAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAUGAGGGCGC------C-GCU
-----..........-...((((.(((((((.......))))))).)))).........((((.(((((((..((((.((......))...)))))))))))------)-))) ( -36.50)
>consensus
____AAAA_UAAUCCUUCUGGAGAUGCGGGGCAUCGAUCCCCGUACCUCUCACAUGCUAAGCGAGCGCUCUACCAUCUGAGCUACAUCCCCGAUGUGAGCGC______C_GCU
....................(((.(((((((.......))))))).)))(((((((((.....)))((((........))))..........))))))............... (-27.73 = -27.90 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:22 2006