Locus 5758

Sequence ID X_DroMel_CAF1
Location 14,937,351 – 14,937,494
Length 143
Max. P 0.997000
window9344 window9345 window9346

overview

Window 4

Location 14,937,351 – 14,937,461
Length 110
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 82.83
Mean single sequence MFE -32.04
Consensus MFE -21.60
Energy contribution -25.35
Covariance contribution 3.75
Combinations/Pair 1.07
Mean z-score -3.65
Structure conservation index 0.67
SVM decision value 2.78
SVM RNA-class probability 0.997000
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14937351 110 + 22224390
AUAAAUGAAAGACCUUGAUAUUUUUAUUUCGUUGUUUGGG-UCACCAAACAGCGAAUAGAAAAGC--AAAGGGUGUCACCUGAAUGGUGUUGAUCUGGGUCAACCAAUAUCAU
..........(((((.(((.((((((((.((((((((((.-...))))))))))))))))))...--.........((((.....))))...))).)))))............ ( -35.00)
>DroSim_CAF1 2088 110 + 1
AUAAAUGAAAGACCUUGAUAUUUUUAUUUCGUUGUUUGGG-UCACCAAACAGCGAAUAGAAAAGC--AAAGGGUGUCACCUGAAUGGUGUUGAUCUGGAUCAACCAAUAUCAU
....((((...(((((....(((((..((((((((((((.-...))))))))))))..)))))..--..)))))...(((.....)))((((((....)))))).....)))) ( -34.20)
>DroEre_CAF1 1828 104 + 1
AUAAAUGAGAGACCUUGAUAUUUUCAUCUUGUUGUUUGGGUUCACCAAACAGCGAAUAGAAAAGC--AAAGGGUGUCACCUGAAUGGUGUUGAUCUGGGUCAA-------CAU
........((.(((((....(((((...(((((((((((.....)))))))))))...)))))..--..))))).))(((.....)))((((((....)))))-------).. ( -37.10)
>DroYak_CAF1 2142 90 + 1
AUAAAUGAGAGACCUUGAUAUUAU----------------UUCACCAAACAGCGAAGUGAAAAGGCAAAAGGGUGUCACCUCAAUGGUGUUGAUCUGGGUCAA-------CAU
........((.(((((.......(----------------(((((...........)))))).......))))).))(((.....)))((((((....)))))-------).. ( -21.84)
>consensus
AUAAAUGAAAGACCUUGAUAUUUUUAUUUCGUUGUUUGGG_UCACCAAACAGCGAAUAGAAAAGC__AAAGGGUGUCACCUGAAUGGUGUUGAUCUGGGUCAA_______CAU
..........(((((.(((.(((((..((((((((((((.....))))))))))))..))))).............((((.....))))...))).)))))............ (-21.60 = -25.35 +   3.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 14,937,351 – 14,937,461
Length 110
Sequences 4
Columns 113
Reading direction reverse
Mean pairwise identity 82.83
Mean single sequence MFE -23.26
Consensus MFE -14.84
Energy contribution -14.65
Covariance contribution -0.19
Combinations/Pair 1.06
Mean z-score -2.26
Structure conservation index 0.64
SVM decision value 0.89
SVM RNA-class probability 0.874708
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14937351 110 - 22224390
AUGAUAUUGGUUGACCCAGAUCAACACCAUUCAGGUGACACCCUUU--GCUUUUCUAUUCGCUGUUUGGUGA-CCCAAACAACGAAAUAAAAAUAUCAAGGUCUUUCAUUUAU
.......(((..((((..(((...((((.....)))).........--.........((((.(((((((...-.))))))).))))........)))..))))..)))..... ( -26.40)
>DroSim_CAF1 2088 110 - 1
AUGAUAUUGGUUGAUCCAGAUCAACACCAUUCAGGUGACACCCUUU--GCUUUUCUAUUCGCUGUUUGGUGA-CCCAAACAACGAAAUAAAAAUAUCAAGGUCUUUCAUUUAU
.((((((((((((((....)))).((((.....))))..)))....--.........((((.(((((((...-.))))))).)))).....)))))))............... ( -25.90)
>DroEre_CAF1 1828 104 - 1
AUG-------UUGACCCAGAUCAACACCAUUCAGGUGACACCCUUU--GCUUUUCUAUUCGCUGUUUGGUGAACCCAAACAACAAGAUGAAAAUAUCAAGGUCUCUCAUUUAU
(((-------..((((..(((...((((.....)))).........--..(((((...((..(((((((.....)))))))....)).))))).)))..))))...))).... ( -22.40)
>DroYak_CAF1 2142 90 - 1
AUG-------UUGACCCAGAUCAACACCAUUGAGGUGACACCCUUUUGCCUUUUCACUUCGCUGUUUGGUGAA----------------AUAAUAUCAAGGUCUCUCAUUUAU
(((-------..((((..(((...(((((.((((((((...............)))))))).....)))))..----------------.....)))..))))...))).... ( -18.36)
>consensus
AUG_______UUGACCCAGAUCAACACCAUUCAGGUGACACCCUUU__GCUUUUCUAUUCGCUGUUUGGUGA_CCCAAACAACGAAAUAAAAAUAUCAAGGUCUCUCAUUUAU
............((((..(((...((((.....)))).....................(((((....)))))......................)))..)))).......... (-14.84 = -14.65 +  -0.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 14,937,387 – 14,937,494
Length 107
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 88.37
Mean single sequence MFE -26.68
Consensus MFE -17.08
Energy contribution -17.07
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.64
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14937387 107 + 22224390
UGGG-UCACCAAACAGCGAAUAGAAAAGC--AAAGGGUGUCACCUGAAUGGUGUUGAUCUGGGUCAACCAAUAUCAUACCAAUGGAACACCAGACCCCAAAAAAUGACGG
.(((-((........((..........))--....(((((..((....((((((.(((.(((.....)))..)))))))))..)).))))).)))))............. ( -29.50)
>DroSim_CAF1 2124 106 + 1
UGGG-UCACCAAACAGCGAAUAGAAAAGC--AAAGGGUGUCACCUGAAUGGUGUUGAUCUGGAUCAACCAAUAUCAUACCAAUGGAACACCAGACCCCAA-AAAUGACGG
.(((-((........((..........))--....(((((..((....((((((.(((.(((.....)))..)))))))))..)).))))).)))))...-......... ( -28.20)
>DroEre_CAF1 1864 100 + 1
UGGGUUCACCAAACAGCGAAUAGAAAAGC--AAAGGGUGUCACCUGAAUGGUGUUGAUCUGGGUCAA-------CAUACCAAUAGAACACCAGACCCCAG-AAAUGACGG
((((.((........((..........))--....(((((...(((..((((((((((....)))))-------)..)))).))).))))).)).)))).-......... ( -25.30)
>DroYak_CAF1 2166 99 + 1
----UUCACCAAACAGCGAAGUGAAAAGGCAAAAGGGUGUCACCUCAAUGGUGUUGAUCUGGGUCAA-------CAUACCAAUGGAACACCAGACCCCAAAAAAUGACGG
----(((((...........))))).........(((.(((.......((((((((((....)))))-------)..)))).(((....)))))))))............ ( -23.70)
>consensus
UGGG_UCACCAAACAGCGAAUAGAAAAGC__AAAGGGUGUCACCUGAAUGGUGUUGAUCUGGGUCAA_______CAUACCAAUGGAACACCAGACCCCAA_AAAUGACGG
..................................(((.(((.......(((((((....(((................)))....)))))))))))))............ (-17.08 = -17.07 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:43 2006