Locus 5362

Sequence ID	X_DroMel_CAF1
Location	13,958,084 – 13,958,316
Length	232
Max. P	0.776559

overview

Window 1

Location	13,958,084 – 13,958,204
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	97.76
Mean single sequence MFE	-28.13
Consensus MFE	-24.70
Energy contribution	-24.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	0.88
SVM decision value	0.17
SVM RNA-class probability	0.615036
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13958084 120 + 22224390
GGUCUUUGUGGCGACCAUGAAAAACGUGACAUUUUUAUGUUGCAAACUUUAAAUCUUUCAUAUCACAAAAUGAAAUGUUGCAAUGCAAUUGACUGCAACAGCAGCGGCUGCAACAACAAC
((((........)))).........(..((((....))))..)............((((((........))))))(((((...((((.(((.((((....))))))).)))).))))).. ( -29.80)
>DroSec_CAF1 9255 117 + 1
GGUCUUUGUGGCGACCAUGAAAAACGUGACAUUUUUAUGUUGCAAACUUUAAAUCUUUCAUAUCAGAAAAUGAAAUGUUGCAAUGCAAUUGACUGCAACAGCAGCGG---CAACAACAAC
((((........)))).........(..((((....))))..)............((((((........))))))((((((..(((..(((....)))..)))...)---)))))..... ( -27.30)
>DroSim_CAF1 9862 117 + 1
GGUCUUUGUGGCGACCAUGAAAAACGUGACAUUUUUAUGUUGCAAACUUUAAAUCUUUCAUAUCAGAAAAUGAAAUGUUGCAAUGCAAUUGACUGCAACAGCAGCGG---CAACAACAAC
((((........)))).........(..((((....))))..)............((((((........))))))((((((..(((..(((....)))..)))...)---)))))..... ( -27.30)
>consensus
GGUCUUUGUGGCGACCAUGAAAAACGUGACAUUUUUAUGUUGCAAACUUUAAAUCUUUCAUAUCAGAAAAUGAAAUGUUGCAAUGCAAUUGACUGCAACAGCAGCGG___CAACAACAAC
((((........)))).........(..((((....))))..)............((((((........))))))((((((..((((......))))...)))))).............. (-24.70 = -24.70 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	13,958,124 – 13,958,242
Length	118
Sequences	3
Columns	118
Reading direction	forward
Mean pairwise identity	94.24
Mean single sequence MFE	-23.37
Consensus MFE	-17.93
Energy contribution	-18.27
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.61
Structure conservation index	0.77
SVM decision value	0.11
SVM RNA-class probability	0.586948
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13958124 118 + 22224390
UGCAAACUUUAAAUCUUUCAUAUCACAAAAUGAAAUGUUGCAAUGCAAUUGACUGCAACAGCAGCGGCUGCAACAACAACGUUGGCAUUUUCAGCCAACAACAACAACAACCAUUCAU
...............((((((........))))))(((((...((((.(((.((((....))))))).))))........((((((.......))))))..)))))............ ( -27.70)
>DroSec_CAF1 9295 111 + 1
UGCAAACUUUAAAUCUUUCAUAUCAGAAAAUGAAAUGUUGCAAUGCAAUUGACUGCAACAGCAGCGG---CAACAACAACGUUGGCAUUUUCAGU----GACAACAACAACCAUUCAU
...............((((......))))(((((.((((((..(((..(((....)))..)))...)---))))).....((((.(((.....))----).))))........))))) ( -21.20)
>DroSim_CAF1 9902 111 + 1
UGCAAACUUUAAAUCUUUCAUAUCAGAAAAUGAAAUGUUGCAAUGCAAUUGACUGCAACAGCAGCGG---CAACAACAACGUUGGCAUUUUCAGU----GACAACAACAACCAUUCAU
...............((((......))))(((((.((((((..(((..(((....)))..)))...)---))))).....((((.(((.....))----).))))........))))) ( -21.20)
>consensus
UGCAAACUUUAAAUCUUUCAUAUCAGAAAAUGAAAUGUUGCAAUGCAAUUGACUGCAACAGCAGCGG___CAACAACAACGUUGGCAUUUUCAGU____GACAACAACAACCAUUCAU
.........................(((((((...((((((..((((......))))...))))))....((((......)))).))))))).......................... (-17.93 = -18.27 +   0.33)

alignment

secondary structure

dotplot

Window 3

Location	13,958,204 – 13,958,316
Length	112
Sequences	3
Columns	112
Reading direction	forward
Mean pairwise identity	93.07
Mean single sequence MFE	-31.97
Consensus MFE	-26.08
Energy contribution	-26.53
Covariance contribution	0.45
Combinations/Pair	1.04
Mean z-score	-2.59
Structure conservation index	0.82
SVM decision value	0.54
SVM RNA-class probability	0.776559
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13958204 112 + 22224390
GUUGGCAUUUUCAGCCAACAACAACAACAACCAUUCAUGUGCACAUGGUUCUCAGUUCUUUGGCAUCUUUUUGUUGUCUUUGAUUGGGAUUUUUGUGUGCUGGUGGCUUUGC
((((((.......))))))...........((((.((.(..((((....((((((((....((((.(.....).))))...))))))))....))))..)))))))...... ( -34.20)
>DroSec_CAF1 9372 107 + 1
GUUGGCAUUUUCAGU----GACAACAACAACCAUUCAUGUGCACAUG-UGCCCAGUUCUUUGGCAUCUUUUUGUUGUCUUUGAUUAGGAUUUUUGUGUGCUGGUGGCUUUGC
((((.(((.....))----).)))).....((((.((.(..((((..-..((.((((....((((.(.....).))))...)))).)).....))))..)))))))...... ( -24.60)
>DroSim_CAF1 9979 108 + 1
GUUGGCAUUUUCAGU----GACAACAACAACCAUUCAUGUGCACAUGCUUCCCAGUUCUUUGGCAGCUUUUUGUUGUCUUUGAUUGGGAUUUUUGUGUGCUGGUGGCUUUGC
((((.(((.....))----).)))).....((((.((.(..((((....((((((((....((((((.....))))))...))))))))....))))..)))))))...... ( -37.10)
>consensus
GUUGGCAUUUUCAGU____GACAACAACAACCAUUCAUGUGCACAUG_UUCCCAGUUCUUUGGCAUCUUUUUGUUGUCUUUGAUUGGGAUUUUUGUGUGCUGGUGGCUUUGC
((((.................)))).....((((.((.(..((((....((((((((....((((.(.....).))))...))))))))....))))..)))))))...... (-26.08 = -26.53 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:09 2006