Locus 5307

Sequence ID 3L_DroMel_CAF1
Location 14,667,548 – 14,667,747
Length 199
Max. P 0.993937
window8388 window8389 window8390

overview

Window 8

Location 14,667,548 – 14,667,649
Length 101
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.30
Mean single sequence MFE -25.29
Consensus MFE -14.04
Energy contribution -14.23
Covariance contribution 0.20
Combinations/Pair 1.07
Mean z-score -1.99
Structure conservation index 0.56
SVM decision value -0.04
SVM RNA-class probability 0.513327
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14667548 101 + 23771897
CCACUUGAAAUGUAUACCCAACAGGGAGUCGAA--ACUGGGACUCCCGACCAUUCCAU---UCAG-------CAACCAGGAUCCAUGAC---AACCCCUCGAGCACCCAU----CUUACA
...(((((...............(((((((...--.....)))))))...((((((..---....-------......)))...)))..---......))))).......----...... ( -18.40)
>DroSec_CAF1 17303 101 + 1
CCACUUGAAAUGUAUACCCAACAGGGAGUCGAA--ACUGGGACUCCCGACCAUGCCAU---CCAG-------CAACCAGGAUCCAUGAC---AACCCCUAGAGCACCCAG----CUUCCA
..........(((..........(((((((...--.....)))))))...((((..((---((..-------......)))).))))))---).......((((.....)----)))... ( -23.20)
>DroSim_CAF1 18127 101 + 1
CCACUUGAAAUGUAUACCCAACAGGGAGUCGAA--ACUGGGACUCCCGACCAUGCCAU---CCAG-------CAACCAGGAUCCAUGAC---AACCCCUCGAGCACCCAG----CUUCCA
...(((((...............(((((((...--.....)))))))...((((..((---((..-------......)))).))))..---......))))).......----...... ( -23.60)
>DroEre_CAF1 17812 111 + 1
CCACUUGAAAUGUAUACCCAACAGGGAGUCGCA--ACUGGGACUCCCGACCAUGCCAUCAUCCAGGCAUGGCAAACCAGGAUCCAUGAC---AACCCCUCGAGCUCCCAG----CUUCCA
....(((..(((.((.((.....(((((((.(.--...).)))))))(.(((((((........))))))))......)))).)))..)---))......((((.....)----)))... ( -34.60)
>DroYak_CAF1 18094 101 + 1
CCACUUGAAAUGUAUACCCAACAGGGAGUCGGA--GCUGCGACUCCCAACUAUGCCAU---CCAG-------CAACCAGGAUCCAUGAC---AACCCCUCGAGCACCCAU----CUUCCA
...(((((...............((((((((..--....))))))))...((((..((---((..-------......)))).))))..---......))))).......----...... ( -23.90)
>DroAna_CAF1 14816 110 + 1
CCACUUGAAAUGGAUACCCAACAGGGAGUCCCAGUAUUGUGACUCCCAACUGCCCCAU---CCAA-------CCACCAAAUUCUGAAACUGGAGCUCCUGGGUCUCCUGAACUCCUGACU
...........(((.(((((...(((((((.(......).)))))))....((.(((.---....-------.................))).))...))))).)))............. ( -28.05)
>consensus
CCACUUGAAAUGUAUACCCAACAGGGAGUCGAA__ACUGGGACUCCCGACCAUGCCAU___CCAG_______CAACCAGGAUCCAUGAC___AACCCCUCGAGCACCCAG____CUUCCA
...((((...(((.......)))(((((((..........))))))).............................))))........................................ (-14.04 = -14.23 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 14,667,616 – 14,667,714
Length 98
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.73
Mean single sequence MFE -24.50
Consensus MFE -12.61
Energy contribution -13.45
Covariance contribution 0.84
Combinations/Pair 1.24
Mean z-score -2.01
Structure conservation index 0.51
SVM decision value 0.26
SVM RNA-class probability 0.659544
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14667616 98 + 23771897
AUCCAUGAC---AACCCCUCGAGCACCCAU----CUUACAGUU--------------CCCUAUUUUUUCGUCCCCAUGGCCGGACUGGAAAACCUGA-AAUGGAAAACAAUUUCAGCUAC
.((((....---........((((......----......)))--------------)...........((((........))))))))....((((-(((........))))))).... ( -16.10)
>DroSec_CAF1 17371 98 + 1
AUCCAUGAC---AACCCCUAGAGCACCCAG----CUUCCAGUU--------------CCCUAUUUUUCCGUCCCCAUGGGCGGACGGAAAAACCUGA-AAUGGAAAACAAUUUCAGCUAC
.(((((..(---(.......((((.....)----)))......--------------.....(((((((((((((...)).)))))))))))..)).-.)))))................ ( -25.90)
>DroSim_CAF1 18195 98 + 1
AUCCAUGAC---AACCCCUCGAGCACCCAG----CUUCCAGUU--------------CCCUAUUUUUCCGUCCCCAUGGGCGGACGGAAAAACCUGA-AAUGGAAAACAAUUUCAGCUAC
.(((((..(---(.......((((.....)----)))......--------------.....(((((((((((((...)).)))))))))))..)).-.)))))................ ( -25.90)
>DroEre_CAF1 17890 97 + 1
AUCCAUGAC---AACCCCUCGAGCUCCCAG----CUUCCAACU--------------ACCUAUUUUUCCGAC-CCAUGGGCGGGCGGAAAAACCUGA-AAUGGAAAACAAUUUCAGCUAC
.(((((..(---(.......((((.....)----)))......--------------.....((((((((.(-((......)))))))))))..)).-.)))))................ ( -23.40)
>DroYak_CAF1 18162 112 + 1
AUCCAUGAC---AACCCCUCGAGCACCCAU----CUUCCAGCUCCCAGCAUACAGUUCCCUAUUUUUCCGUCCCCAUGGGCGGGCGGAAAAACCUGA-AAUGGAAAACAAUUUCAGCUAC
.........---........((((......----......))))..(((.............(((((((((((((...)).)))))))))))..(((-(((........))))))))).. ( -27.10)
>DroAna_CAF1 14886 105 + 1
UUCUGAAACUGGAGCUCCUGGGUCUCCUGAACUCCUGACUCCU--------------CGCAGCUUCUAGCUCCCCGCGGGCGGUG-GGAAAACCUGAAAAUGGAAAACAAUUUCAGCUAC
..........((((((....)).)))).....((((.(((.((--------------((((((.....)))....))))).))))-)))....((((((.((.....)).)))))).... ( -28.60)
>consensus
AUCCAUGAC___AACCCCUCGAGCACCCAG____CUUCCAGCU______________CCCUAUUUUUCCGUCCCCAUGGGCGGACGGAAAAACCUGA_AAUGGAAAACAAUUUCAGCUAC
.....................(((......................................(((((((((((((...)).)))))))))))........(((((.....)))))))).. (-12.61 = -13.45 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 14,667,649 – 14,667,747
Length 98
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 85.84
Mean single sequence MFE -27.66
Consensus MFE -22.62
Energy contribution -22.78
Covariance contribution 0.16
Combinations/Pair 1.14
Mean z-score -2.71
Structure conservation index 0.82
SVM decision value 2.44
SVM RNA-class probability 0.993937
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14667649 98 + 23771897
GUU--------------CCCUAUUUUUUCGUCCCCAUGGCCGGACUGGAAAACCUGAAAUGGAAAACAAUUUCAGCUACGCAAACACGGCGGGAAGGCCAACACAAAA----AAAA
.((--------------(((...((((((((((........)))).)))))).(((((((........)))))))....((.......))))))).............----.... ( -21.30)
>DroSec_CAF1 17404 95 + 1
GUU--------------CCCUAUUUUUCCGUCCCCAUGGGCGGACGGAAAAACCUGAAAUGGAAAACAAUUUCAGCUACGCAAACACGGCGGGAAGGCCAACACAAAA-------A
.((--------------(((..(((((((((((((...)).))))))))))).(((((((........)))))))....((.......))))))).............-------. ( -30.80)
>DroSim_CAF1 18228 96 + 1
GUU--------------CCCUAUUUUUCCGUCCCCAUGGGCGGACGGAAAAACCUGAAAUGGAAAACAAUUUCAGCUACGCAAACACGGCGGGAAGGCCAACACAAAA------AA
.((--------------(((..(((((((((((((...)).))))))))))).(((((((........)))))))....((.......))))))).............------.. ( -30.80)
>DroEre_CAF1 17923 101 + 1
ACU--------------ACCUAUUUUUCCGAC-CCAUGGGCGGGCGGAAAAACCUGAAAUGGAAAACAAUUUCAGCUACGCAAACACGGCGAGAAGGCCAACACAAAAUCACAAAA
...--------------.(((.((((((((.(-((......))))))))))).(((((((........)))))))((.(((.......))))).)))................... ( -25.40)
>DroYak_CAF1 18195 107 + 1
GCUCCCAGCAUACAGUUCCCUAUUUUUCCGUCCCCAUGGGCGGGCGGAAAAACCUGAAAUGGAAAACAAUUUCAGCUACGCAAACACGGCGAGAAGGCCAACACAA---------A
.......((.............(((((((((((((...)).))))))))))).(((((((........)))))))....))......(((......))).......---------. ( -30.00)
>consensus
GUU______________CCCUAUUUUUCCGUCCCCAUGGGCGGACGGAAAAACCUGAAAUGGAAAACAAUUUCAGCUACGCAAACACGGCGGGAAGGCCAACACAAAA______AA
......................(((((((((((........))))))))))).(((((((........)))))))............(((......)))................. (-22.62 = -22.78 +   0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:53 2006