Locus 4887

Sequence ID	X_DroMel_CAF1
Location	12,704,338 – 12,704,601
Length	263
Max. P	0.999315

overview

Window 5

Location	12,704,338 – 12,704,444
Length	106
Sequences	3
Columns	113
Reading direction	reverse
Mean pairwise identity	93.47
Mean single sequence MFE	-26.97
Consensus MFE	-21.37
Energy contribution	-21.82
Covariance contribution	0.45
Combinations/Pair	1.04
Mean z-score	-2.52
Structure conservation index	0.79
SVM decision value	0.28
SVM RNA-class probability	0.666945
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12704338 106 - 22224390
CUUUUUCCGGCCAUCUGGUUG-GAAUACUGGUCCAUAAAGUUUAAUGAUCCAUACACAACGAAGCUCCUAAAGUUAGAUUUCGGCAAAACUUAUCUUUUUGCCAUUU------
....((((((((....)))))-)))...(((..(((........)))..)))........((((...(((....))).))))(((((((.......)))))))....------ ( -22.70)
>DroSec_CAF1 57062 111 - 1
CUUUUUCCGGCCAUCUGGCUGGGAAUACUGGUCCAUAAAGUUUAAUGAUCCAUACACAACGAAGCUCCUAAAGUGAGAUUUCGGCAAAACUUAUCUU--UGCCAUUUUUAUAU
...(((((((((....)))))))))...(((..(((........)))..)))........((((((((....).))).))))((((((.......))--)))).......... ( -29.10)
>DroSim_CAF1 43557 111 - 1
CUUUUUCCGGCCAUCUGGCUGGGAAUACUGGUCCAUAAAGUUUAAUGAUCCAUACACAACGAAGCUCCUAAAGUGAGAUUUCGGCAAAACUUAUCUU--UGCCAUUUUUAUAU
...(((((((((....)))))))))...(((..(((........)))..)))........((((((((....).))).))))((((((.......))--)))).......... ( -29.10)
>consensus
CUUUUUCCGGCCAUCUGGCUGGGAAUACUGGUCCAUAAAGUUUAAUGAUCCAUACACAACGAAGCUCCUAAAGUGAGAUUUCGGCAAAACUUAUCUU__UGCCAUUUUUAUAU
...(((((((((....)))))))))...(((..(((........)))..)))........(((((((.......))).))))((((.............)))).......... (-21.37 = -21.82 +   0.45)

alignment

secondary structure

dotplot

Window 6

Location	12,704,405 – 12,704,524
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.36
Mean single sequence MFE	-36.10
Consensus MFE	-23.36
Energy contribution	-27.05
Covariance contribution	3.69
Combinations/Pair	1.22
Mean z-score	-3.31
Structure conservation index	0.65
SVM decision value	2.79
SVM RNA-class probability	0.997067
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12704405 119 - 22224390
AGGAUAUUCUAUAGAAAUACUCCAAAUUACAUCGUGACAUCUGAUAUGAUUUUGUUUGGGAAAGUCCAUGCAGCAAUGCACUUUUUCCGGCCAUCUGGUUG-GAAUACUGGUCCAUAAAG
.((((.(((..((....))..((((((...((((((.(....).))))))...))))))))).))))..(((....)))(((..((((((((....)))))-)))....)))........ ( -31.90)
>DroSec_CAF1 57133 120 - 1
AGGACAUUCUAUAGAAAUACUCCAAAUGGCAUCAUGACAUCUGAUAUGAUGUUGUUUGGGAAAGUCCAUGCAGCAAUGCACUUUUUCCGGCCAUCUGGCUGGGAAUACUGGUCCAUAAAG
.((((.(((..((....))..(((((..((((((((.(....).))))))))..)))))))).)))).((((....))))...(((((((((....)))))))))............... ( -44.80)
>DroSim_CAF1 43628 120 - 1
AGGACAUUCUAUAGAAAUACUCGAAAUGACAUCAUGACAUCUGAUAUGAUGUUGUUUGGGAAAGUCCGUGCAGCAAUGCACUUUUUCCGGCCAUCUGGCUGGGAAUACUGGUCCAUAAAG
.((((.(((....)))...(((.(((..((((((((.(....).))))))))..))))))...))))(((((....)))))..(((((((((....)))))))))............... ( -44.00)
>DroEre_CAF1 56652 98 - 1
AGGACAUUCUAUAGGAAUACUCCAAAUGACAUCAUGACAUUUGAUAUCCUGUCUAU--------AUC--------AUGCAC-UUUUCCGGCCAUCUGGAUG-GAGUACUGGAAUGU----
...((((((((......(((((((........(((((.((..(((.....))).))--------.))--------)))...-...(((((....)))))))-))))).))))))))---- ( -23.70)
>consensus
AGGACAUUCUAUAGAAAUACUCCAAAUGACAUCAUGACAUCUGAUAUGAUGUUGUUUGGGAAAGUCCAUGCAGCAAUGCACUUUUUCCGGCCAUCUGGCUG_GAAUACUGGUCCAUAAAG
.((((.(((....)))....((((((((((((((((.(....).))))))))))))))))...)))).((((....))))...(((((((((....)))))))))............... (-23.36 = -27.05 +   3.69)

alignment

secondary structure

dotplot

Window 7

Location	12,704,444 – 12,704,561
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.99
Mean single sequence MFE	-35.75
Consensus MFE	-23.92
Energy contribution	-26.55
Covariance contribution	2.63
Combinations/Pair	1.16
Mean z-score	-3.89
Structure conservation index	0.67
SVM decision value	3.51
SVM RNA-class probability	0.999315
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12704444 117 - 22224390
UCGGUAGAGCGG---UAUUUUUAAGUCUAGGAUGUCAGAAAGGAUAUUCUAUAGAAAUACUCCAAAUUACAUCGUGACAUCUGAUAUGAUUUUGUUUGGGAAAGUCCAUGCAGCAAUGCA
..((.....(((---((((((((....(((((((((......)))))))))))))))))))((((((...((((((.(....).))))))...))))))).....)).((((....)))) ( -30.90)
>DroSec_CAF1 57173 115 - 1
UCGGUAGAGCGG---UAUUCU--AGUCUAGAAUGUCUGAAAGGACAUUCUAUAGAAAUACUCCAAAUGGCAUCAUGACAUCUGAUAUGAUGUUGUUUGGGAAAGUCCAUGCAGCAAUGCA
..((.....(((---((((((--(...((((((((((....))))))))))))).))))))(((((..((((((((.(....).))))))))..)))))).....)).((((....)))) ( -43.70)
>DroSim_CAF1 43668 115 - 1
UCGGUAGAGCGG---UAUUCU--AUUCUAGAAUGUCUGAAAGGACAUUCUAUAGAAAUACUCGAAAUGACAUCAUGACAUCUGAUAUGAUGUUGUUUGGGAAAGUCCGUGCAGCAAUGCA
........((((---..((((--(...((((((((((....)))))))))))))))...(((.(((..((((((((.(....).))))))))..)))))).....))))(((....))). ( -40.80)
>DroEre_CAF1 56686 102 - 1
UCAGUAAAGGGGGGCUAUUCU--AGUCUAGAAUGUCUAAAAGGACAUUCUAUAGGAAUACUCCAAAUGACAUCAUGACAUUUGAUAUCCUGUCUAU--------AUC--------AUGCA
...((.....((((.((((((--....((((((((((....))))))))))..)))))))))).....))..(((((.((..(((.....))).))--------.))--------))).. ( -27.60)
>consensus
UCGGUAGAGCGG___UAUUCU__AGUCUAGAAUGUCUGAAAGGACAUUCUAUAGAAAUACUCCAAAUGACAUCAUGACAUCUGAUAUGAUGUUGUUUGGGAAAGUCCAUGCAGCAAUGCA
...(((..((.................((((((((((....)))))))))).........((((((((((((((((.(....).))))))))))))))))............))..))). (-23.92 = -26.55 +   2.63)

alignment

secondary structure

dotplot

Window 8

Location	12,704,484 – 12,704,601
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	85.82
Mean single sequence MFE	-25.03
Consensus MFE	-16.55
Energy contribution	-16.05
Covariance contribution	-0.50
Combinations/Pair	1.32
Mean z-score	-2.08
Structure conservation index	0.66
SVM decision value	0.50
SVM RNA-class probability	0.759904
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12704484 117 - 22224390
UGAUUUCGAUUAAAUUACAAAAUAUAAUAAUACUCGUUUUUCGGUAGAGCGG---UAUUUUUAAGUCUAGGAUGUCAGAAAGGAUAUUCUAUAGAAAUACUCCAAAUUACAUCGUGACAU
..............((((................((((((.....))))))(---((((((((....(((((((((......)))))))))))))))))).............))))... ( -20.50)
>DroSec_CAF1 57213 115 - 1
UGAUUUCGAUUAAAUUACAAAAUAUAAUAAUACUCGUUUUUCGGUAGAGCGG---UAUUCU--AGUCUAGAAUGUCUGAAAGGACAUUCUAUAGAAAUACUCCAAAUGGCAUCAUGACAU
((((.(((......................(((.((((((.....)))))))---))((((--(...((((((((((....)))))))))))))))..........))).))))...... ( -25.80)
>DroSim_CAF1 43708 115 - 1
UGAUUUUGAUAAAAUUACAAAAUAUAAUAAUACUCGUUUUUCGGUAGAGCGG---UAUUCU--AUUCUAGAAUGUCUGAAAGGACAUUCUAUAGAAAUACUCGAAAUGACAUCAUGACAU
..(((((((.....................(((.((((((.....)))))))---))((((--(...((((((((((....)))))))))))))))....)))))))............. ( -27.10)
>DroEre_CAF1 56710 118 - 1
UGAUUUCAAUAAAAUUAAAAAGUAGUUUAUUACCAUAUUCUCAGUAAAGGGGGGCUAUUCU--AGUCUAGAAUGUCUAAAAGGACAUUCUAUAGGAAUACUCCAAAUGACAUCAUGACAU
((((.(((...((((((.....))))))......................((((.((((((--....((((((((((....))))))))))..))))))))))...))).))))...... ( -26.70)
>consensus
UGAUUUCGAUAAAAUUACAAAAUAUAAUAAUACUCGUUUUUCGGUAGAGCGG___UAUUCU__AGUCUAGAAUGUCUGAAAGGACAUUCUAUAGAAAUACUCCAAAUGACAUCAUGACAU
..(((((..........................(((((((.....)))))))...............((((((((((....))))))))))..)))))...................... (-16.55 = -16.05 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:24 2006