Locus 4694

Sequence ID X_DroMel_CAF1
Location 12,224,598 – 12,224,723
Length 125
Max. P 0.699334
window7701 window7702 window7703

overview

Window 1

Location 12,224,598 – 12,224,689
Length 91
Sequences 4
Columns 100
Reading direction forward
Mean pairwise identity 90.92
Mean single sequence MFE -19.88
Consensus MFE -15.80
Energy contribution -16.30
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.49
Structure conservation index 0.79
SVM decision value 0.03
SVM RNA-class probability 0.548202
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12224598 91 + 22224390
UCAACGGGUAGCAAAACGAGACUAAAAGGACC---------AGGCCAAAAAGGACUUGGCCCAGGGAAAACUCUAUUUUCACACGGCAACAAAAUGCUGA
........(((((....((((......((.((---------(((((.....)).))))).))((((....))))..))))....(....)....))))). ( -21.70)
>DroSec_CAF1 47420 90 + 1
UCAACGGGUAGCAAAACGAGACUAAAAAGACC---------AGGCCAAAAAGGACUUGGCCCAGGGA-AACUCUAUUUUCACACGGCAACAAAAUGCUGA
.....(((((((.......).)))......((---------(((((.....)).))))))))(((..-..).)).........(((((......))))). ( -19.10)
>DroEre_CAF1 44793 91 + 1
UCAACGGGUAGCAAAACGAGACUAAAAAGACU---------AGGCCAAAAAGGACAUGGCCCAGGGAAAACUCUAUUUUCACACGGCAACAAAAUGCUGC
.......((((((....((((.........((---------.(((((.........))))).))(((....)))..))))....(....)....)))))) ( -19.10)
>DroYak_CAF1 31970 100 + 1
UCAACGGGUAGCCAAACGAGACUAAAAAGACUAAAAAGUCCAGGCCAAAAUGGACUUGGCCCAGGGAAAACUCUAUUUUCACACCGCAACAAAAUGCUGA
......(((..((...............((((....))))..((((((.......))))))..))(((((.....)))))..)))(((......)))... ( -19.60)
>consensus
UCAACGGGUAGCAAAACGAGACUAAAAAGACC_________AGGCCAAAAAGGACUUGGCCCAGGGAAAACUCUAUUUUCACACGGCAACAAAAUGCUGA
.................((((.....................((((((.......)))))).((((....))))..))))...(((((......))))). (-15.80 = -16.30 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 12,224,628 – 12,224,723
Length 95
Sequences 4
Columns 106
Reading direction forward
Mean pairwise identity 87.06
Mean single sequence MFE -21.90
Consensus MFE -15.21
Energy contribution -16.02
Covariance contribution 0.81
Combinations/Pair 1.05
Mean z-score -1.69
Structure conservation index 0.69
SVM decision value 0.19
SVM RNA-class probability 0.627127
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12224628 95 + 22224390
CC---------AGGCCAAAAAGGACUUGGCCCAGGGAAAACUCUAUUUUCACACGGCAACAAAAUGCUGAGAUAAUACGGAA--CCAGUCCAUGAUUUAUAGACUU
((---------.((((((.......))))))...)).....(((((..(((..(((((......))))).........(((.--....))).)))...)))))... ( -23.20)
>DroSec_CAF1 47450 94 + 1
CC---------AGGCCAAAAAGGACUUGGCCCAGGGA-AACUCUAUUUUCACACGGCAACAAAAUGCUGAGAUAAUACUGAA--CCAGUCCAUGAUUUAUAGACUU
((---------.((((((.......))))))...)).-...(((((..(((..(((((......))))).......((((..--.))))...)))...)))))... ( -21.30)
>DroEre_CAF1 44823 95 + 1
CU---------AGGCCAAAAAGGACAUGGCCCAGGGAAAACUCUAUUUUCACACGGCAACAAAAUGCUGCGAUAAUAUGGAA--CCACUUCGUGAUUUAUAGACCU
((---------.(((((.........))))).)).......(((((..((((.(((((......)))))........((...--.))....))))...)))))... ( -21.60)
>DroYak_CAF1 32000 106 + 1
CUAAAAAGUCCAGGCCAAAAUGGACUUGGCCCAGGGAAAACUCUAUUUUCACACCGCAACAAAAUGCUGAGAAAAUAUUGAACACUAGUCCAUGAUUUAUAGACUU
.....(((((..((((((.......))))))((.(((....(((((((((.((..(((......))))).)))))))..)).......))).)).......))))) ( -21.50)
>consensus
CC_________AGGCCAAAAAGGACUUGGCCCAGGGAAAACUCUAUUUUCACACGGCAACAAAAUGCUGAGAUAAUACGGAA__CCAGUCCAUGAUUUAUAGACUU
............((((((.......))))))..........(((((..(((..(((((......))))).........(((.......))).)))...)))))... (-15.21 = -16.02 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 12,224,628 – 12,224,723
Length 95
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 87.06
Mean single sequence MFE -27.25
Consensus MFE -18.89
Energy contribution -18.57
Covariance contribution -0.31
Combinations/Pair 1.12
Mean z-score -1.85
Structure conservation index 0.69
SVM decision value 0.35
SVM RNA-class probability 0.699334
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12224628 95 - 22224390
AAGUCUAUAAAUCAUGGACUGG--UUCCGUAUUAUCUCAGCAUUUUGUUGCCGUGUGAAAAUAGAGUUUUCCCUGGGCCAAGUCCUUUUUGGCCU---------GG
.(((((((.....)))))))((--..(..((((.((.(((((......)))..)).)).))))..)....))(..(((((((.....))))))).---------.) ( -25.30)
>DroSec_CAF1 47450 94 - 1
AAGUCUAUAAAUCAUGGACUGG--UUCAGUAUUAUCUCAGCAUUUUGUUGCCGUGUGAAAAUAGAGUU-UCCCUGGGCCAAGUCCUUUUUGGCCU---------GG
((.(((((....(((((((((.--..)))).......((((.....))))))))).....))))).))-...(..(((((((.....))))))).---------.) ( -26.60)
>DroEre_CAF1 44823 95 - 1
AGGUCUAUAAAUCACGAAGUGG--UUCCAUAUUAUCGCAGCAUUUUGUUGCCGUGUGAAAAUAGAGUUUUCCCUGGGCCAUGUCCUUUUUGGCCU---------AG
((.(((((....((((..(((.--...)))......(((((.....))))))))).....))))).))....((((((((.........))))))---------)) ( -27.60)
>DroYak_CAF1 32000 106 - 1
AAGUCUAUAAAUCAUGGACUAGUGUUCAAUAUUUUCUCAGCAUUUUGUUGCGGUGUGAAAAUAGAGUUUUCCCUGGGCCAAGUCCAUUUUGGCCUGGACUUUUUAG
((((((.....((.(((((....))))).(((((((.(((((......)))..)).))))))))).........((((((((.....))))))))))))))..... ( -29.50)
>consensus
AAGUCUAUAAAUCAUGGACUGG__UUCAAUAUUAUCUCAGCAUUUUGUUGCCGUGUGAAAAUAGAGUUUUCCCUGGGCCAAGUCCUUUUUGGCCU_________AG
((.(((((...(((((((......)))............(((......)))...))))..))))).))......((((((((.....))))))))........... (-18.89 = -18.57 +  -0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:31:11 2006