Locus 3747

Sequence ID	X_DroMel_CAF1
Location	9,957,735 – 9,958,012
Length	277
Max. P	0.749026

overview

Window 5

Location	9,957,735 – 9,957,854
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.23
Mean single sequence MFE	-27.91
Consensus MFE	-23.13
Energy contribution	-24.13
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.62
Structure conservation index	0.83
SVM decision value	0.47
SVM RNA-class probability	0.749026
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9957735 119 + 22224390
UUUCUUUCUCUCGCGGCUAUUUGCCAUUUGCCAUUUGCCUUUG-GAACUGAAUGGAGUGGAGCUCCAUGUGUCAUUUUUAUCGCUUCACUCCAUGGUAAACCCAGAAACCCCUAACUUUG
....(((((.....(((.....))).((((((.....((...)-)......((((((((((((...................))))))))))))))))))...)))))............ ( -30.01)
>DroSec_CAF1 25766 112 + 1
UCUCUUUCUCUCGCGGCUAUUUGCC-------AUUUGCCUUUG-GAACAGAAUGGAGUGGAGCUCCAUGUGUCAUUUUUAUCGCUUCACUCCAUGGUAAACCCCGAAACCCCUAACUUUG
..........(((.(((.....)))-------.((((((((((-...))))((((((((((((...................))))))))))))))))))...))).............. ( -28.91)
>DroSim_CAF1 6957 115 + 1
----UUUCUCUCGCGGCUAUUUGCCAUUUGCCAUUUGCCUUUG-GAACAGAAUGGAGUGGAGCUCCAUGUGUCAUUUUUAUCGCUUCACUCCAUGGUAAACCCCGAAACCCCUAACUUUG
----......(((.((...((((((.(((((((........))-)..))))((((((((((((...................)))))))))))))))))).))))).............. ( -31.31)
>DroEre_CAF1 20402 110 + 1
GCUCAUUC--UCUCAGCUAUUUGCC-------AUUUGCCUUUGGGAACAGAAUGGAGUGGAGCUCCAUGUGUCAUUUUUAUCGCUUCAGUCCAUGGUAAAGCCCGAAACCCCUAACU-UG
(((.....--....)))..((((..-------.((((((((((....))))(((((.((((((...................)))))).)))))))))))...))))..........-.. ( -25.31)
>DroYak_CAF1 20152 102 + 1
----------UUUCAGCUAUUUGCC-------AUUUGCCUUUG-GAACAGAAUGGAGUGGAGCUCCAUGUGUCAUUUUUAUCGCUUCACUCCACGGUAAACCCCGAAACCCCCAACUUUG
----------.....((.....)).-------........(((-(.......(((((((((((...................)))))))))))(((......)))......))))..... ( -24.01)
>consensus
__UCUUUCUCUCGCGGCUAUUUGCC_______AUUUGCCUUUG_GAACAGAAUGGAGUGGAGCUCCAUGUGUCAUUUUUAUCGCUUCACUCCAUGGUAAACCCCGAAACCCCUAACUUUG
..............(((.....)))........((((((((((....))))((((((((((((...................)))))))))))))))))).................... (-23.13 = -24.13 +   1.00)

alignment

secondary structure

dotplot

Window 6

Location	9,957,854 – 9,957,972
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.90
Mean single sequence MFE	-34.46
Consensus MFE	-23.94
Energy contribution	-23.94
Covariance contribution	-0.00
Combinations/Pair	1.07
Mean z-score	-1.79
Structure conservation index	0.69
SVM decision value	0.01
SVM RNA-class probability	0.536249
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9957854 118 + 22224390
CA--ACCACUCCACCAUGCUCUGCUGGCAUCUCGAAUCCGGAGAUCCGGAGUGCUCCAAGUGGCGCUGCAUAAAAUUGCCAACUACACAAUCGCAGUCUGGCUUGGUUUUUAUGACUCAG
.(--((((.......((((....((((.(((((.......)))))))))((((((......))))))))))......(((((((.(......).))).)))).)))))............ ( -31.20)
>DroSec_CAF1 25878 120 + 1
CAGCACCACUCCACCCUGCCCUGCUGGCAUCUCGAAUCCGGAGAUCCGGAGUGCUCCAAGUGGCGCUGCAUAAAAUUGCCAACUACACAAUCGCUGUCUGGCUUGGUUUUUAUGACUCAG
((((.(((((.(((..((((.....)))).......(((((....)))))))).....))))).))))(((((((..((((((((.(((.....))).))).))))))))))))...... ( -39.30)
>DroSim_CAF1 7072 120 + 1
CAGCACCACUCCACCCUGCCCUGCUGGCAUCUCGAAUCCGGAGAUCCGGAGUGCUCCAAGUGGCGCUGCAUAAAAUUGCCAACUGCACAAUCGCAGUCUGGCUUGGUUUUUAUGACUCAA
((((.(((((.(((..((((.....)))).......(((((....)))))))).....))))).))))(((((((..(((((((((......))))).)))).....)))))))...... ( -44.10)
>DroEre_CAF1 20512 106 + 1
C---ACCACUC---CCCGCCCCCUUGGCAUCCCGAAUUC--------GGAGUGCUCCAAGUGGCGCUGCAUAAAAUUGCCAACUACACAAUCGCAGUCUGGCUUGCUUUUUAUGACUCAG
.---.......---..((((..(((((((..(((....)--------))..)))..)))).))))...(((((((..(((((((.(......).))).)))).....)))))))...... ( -28.90)
>DroYak_CAF1 20254 106 + 1
C---ACCACUC---CCGGCUCUCUUGGCAUCCCGAAUCC--------GGAGUGCUCCAAGUGGCGCUGCAUAAAAUUGCCAACUACACAAUCGCAGUCUGGCUUGGUUUUUAUGACUCAG
.---.......---.((((((.(((((((..(((....)--------))..)))..)))).)).))))(((((((..((((((((.((.......)).))).))))))))))))...... ( -28.80)
>consensus
CA__ACCACUCCACCCUGCCCUGCUGGCAUCUCGAAUCCGGAGAUCCGGAGUGCUCCAAGUGGCGCUGCAUAAAAUUGCCAACUACACAAUCGCAGUCUGGCUUGGUUUUUAUGACUCAG
.....(((((.......(((.....))).....(..(((((....)))))...)....))))).....(((((((..(((((((.(......).))).)))).....)))))))...... (-23.94 = -23.94 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	9,957,892 – 9,958,012
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.14
Mean single sequence MFE	-37.12
Consensus MFE	-34.42
Energy contribution	-34.50
Covariance contribution	0.08
Combinations/Pair	1.05
Mean z-score	-1.17
Structure conservation index	0.93
SVM decision value	0.32
SVM RNA-class probability	0.685048
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9957892 120 + 22224390
GAGAUCCGGAGUGCUCCAAGUGGCGCUGCAUAAAAUUGCCAACUACACAAUCGCAGUCUGGCUUGGUUUUUAUGACUCAGAAGUGCUUUACGCUGUGAUUGAGUAGACAGCCGACCGCAG
.......(((....)))..(((((((((((......)))...((((.((((((((((..(((((((((.....))).)))....)))....)))))))))).))))..)).)).)))).. ( -36.50)
>DroSec_CAF1 25918 120 + 1
GAGAUCCGGAGUGCUCCAAGUGGCGCUGCAUAAAAUUGCCAACUACACAAUCGCUGUCUGGCUUGGUUUUUAUGACUCAGAAGUGCUUUACGCUGUGAUUGAGUAGACAGCCGACCGCAG
.......(((....)))..((((((((((((((((..((((((((.(((.....))).))).))))))))))))((((((.((((.....))))....))))))...))).)).)))).. ( -34.90)
>DroSim_CAF1 7112 120 + 1
GAGAUCCGGAGUGCUCCAAGUGGCGCUGCAUAAAAUUGCCAACUGCACAAUCGCAGUCUGGCUUGGUUUUUAUGACUCAAAAGUGCUUUACGCUGUGAUUGAGUAGACAGCCGACCGCAG
.......(((....)))..((((((((((((((((..(((((((((......))))).)))).....)))))))((((((.((((.....))))....))))))...))).)).)))).. ( -40.00)
>DroEre_CAF1 20545 113 + 1
-------GGAGUGCUCCAAGUGGCGCUGCAUAAAAUUGCCAACUACACAAUCGCAGUCUGGCUUGCUUUUUAUGACUCAGAAGUGCUUUACGCUGUGAUUGAGUAGACAGCCGACCGCAG
-------(((....)))..(((((((((((......)))...((((.((((((((((..(((..((((((........)))))))))....)))))))))).))))..)).)).)))).. ( -38.00)
>DroYak_CAF1 20287 113 + 1
-------GGAGUGCUCCAAGUGGCGCUGCAUAAAAUUGCCAACUACACAAUCGCAGUCUGGCUUGGUUUUUAUGACUCAGAAGUGCUUUACGCUGUGAUUGAGUAGACAGCCGACCGCAG
-------(((....)))..(((((((((((......)))...((((.((((((((((..(((((((((.....))).)))....)))....)))))))))).))))..)).)).)))).. ( -36.20)
>consensus
GAGAUCCGGAGUGCUCCAAGUGGCGCUGCAUAAAAUUGCCAACUACACAAUCGCAGUCUGGCUUGGUUUUUAUGACUCAGAAGUGCUUUACGCUGUGAUUGAGUAGACAGCCGACCGCAG
.......(((....)))..(((((((((((......)))...((((.((((((((((..(((((((((.....))).)))....)))....)))))))))).))))..)).)).)))).. (-34.42 = -34.50 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:27 2006