Locus 944

Sequence ID	X_DroMel_CAF1
Location	2,654,746 – 2,654,843
Length	97
Max. P	0.934511

overview

Window 5

Location	2,654,746 – 2,654,843
Length	97
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	75.37
Mean single sequence MFE	-23.18
Consensus MFE	-13.90
Energy contribution	-13.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.90
Structure conservation index	0.60
SVM decision value	1.24
SVM RNA-class probability	0.934511
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2654746 97 + 22224390
AAGUAAAUCAGCGCUGCCAUUUGCCAUGCCCCGAAAAGUACGAUCCAUGG-AAAAAGUGGCAAAAG-UGGUAAAUGGUCGGUGGUGGUGGUGGGGGGGU
......((((.(((((((((((((((((((.((.......)).((....)-)......))))....-)))))))))).))))).))))........... ( -30.40)
>DroPse_CAF1 97125 78 + 1
AAGUAAAUCAGCGCUGCCAUUUGCCAUGCC-CGAAAAGUAUGCUCCAUGG-AUAAAGUGGCAGUUAACA--G-------------GG----UGGCAGGG
...........(.((((((((((((((..(-((...((....))...)))-.....)))))))......--.-------------.)----)))))).) ( -20.20)
>DroSec_CAF1 61400 75 + 1
AAGUAAAUCAGCGCUGCCAUUUGCCAUGGC-CAAAAAGUACGAUCCAUGGGAAAAAGUGGCAAAUG-UG----------------------CGGCAGGG
............(((((((((((((((..(-(.................)).....))))))))))-.)----------------------)))).... ( -24.53)
>DroEre_CAF1 71197 80 + 1
AAGUAAAUCAGCGCUGCCAUUUGCCAUGCC-CAAAAAGUACGAUCCAUGG-AAAAAGUGGCAAAUG-UGGAGG--------GA--------GGGCAGGA
.......((..(.((.(((((((((((..(-((..............)))-.....))))))))))-.).)).--------).--------.))..... ( -19.64)
>DroYak_CAF1 67397 75 + 1
AAGUAAAUCAGCGCUGCCAUUUGCCAUGCC-CAAAAAAAAGGAUCCAUGG-AAAAAGUGGCAAAUG-UGCGG---------AA--------G----CGG
..........((.((((((((((((((..(-(........)).((....)-)....))))))))))-.))))---------..--------)----).. ( -24.10)
>DroPer_CAF1 114662 78 + 1
AAGUAAAUCAGCGCUGCCAUUUGCCAUGCC-CGAAAAGUAUGCUCCAUGG-AUAAAGUGGCAGUUAACA--G-------------GG----UGGCAGGG
...........(.((((((((((((((..(-((...((....))...)))-.....)))))))......--.-------------.)----)))))).) ( -20.20)
>consensus
AAGUAAAUCAGCGCUGCCAUUUGCCAUGCC_CAAAAAGUACGAUCCAUGG_AAAAAGUGGCAAAUG_UG__G___________________GGGCAGGG
..............((((((((.(((((.................)))))....))))))))..................................... (-13.90 = -13.90 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	2,654,746 – 2,654,843
Length	97
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	75.37
Mean single sequence MFE	-18.12
Consensus MFE	-11.53
Energy contribution	-11.31
Covariance contribution	-0.22
Combinations/Pair	1.07
Mean z-score	-1.34
Structure conservation index	0.64
SVM decision value	0.37
SVM RNA-class probability	0.707840
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2654746 97 - 22224390
ACCCCCCCACCACCACCACCGACCAUUUACCA-CUUUUGCCACUUUUU-CCAUGGAUCGUACUUUUCGGGGCAUGGCAAAUGGCAGCGCUGAUUUACUU
................((.((.((((((.(((-....((((......(-(....))(((.......)))))))))).))))))...)).))........ ( -17.20)
>DroPse_CAF1 97125 78 - 1
CCCUGCCA----CC-------------C--UGUUAACUGCCACUUUAU-CCAUGGAGCAUACUUUUCG-GGCAUGGCAAAUGGCAGCGCUGAUUUACUU
..((((((----..-------------.--(((((..((((.(((((.-...)))))....(.....)-)))))))))..))))))............. ( -16.30)
>DroSec_CAF1 61400 75 - 1
CCCUGCCG----------------------CA-CAUUUGCCACUUUUUCCCAUGGAUCGUACUUUUUG-GCCAUGGCAAAUGGCAGCGCUGAUUUACUU
....((.(----------------------(.-(((((((((..........(((.(((.......))-))))))))))))))).))............ ( -19.80)
>DroEre_CAF1 71197 80 - 1
UCCUGCCC--------UC--------CCUCCA-CAUUUGCCACUUUUU-CCAUGGAUCGUACUUUUUG-GGCAUGGCAAAUGGCAGCGCUGAUUUACUU
..(((((.--------..--------......-.((((((((.....(-(((..((......))..))-))..)))))))))))))............. ( -17.30)
>DroYak_CAF1 67397 75 - 1
CCG----C--------UU---------CCGCA-CAUUUGCCACUUUUU-CCAUGGAUCCUUUUUUUUG-GGCAUGGCAAAUGGCAGCGCUGAUUUACUU
.((----(--------(.---------..((.-(((((((((.....(-(((..((......))..))-))..)))))))))))))))........... ( -21.80)
>DroPer_CAF1 114662 78 - 1
CCCUGCCA----CC-------------C--UGUUAACUGCCACUUUAU-CCAUGGAGCAUACUUUUCG-GGCAUGGCAAAUGGCAGCGCUGAUUUACUU
..((((((----..-------------.--(((((..((((.(((((.-...)))))....(.....)-)))))))))..))))))............. ( -16.30)
>consensus
CCCUGCCC___________________C__CA_CAUUUGCCACUUUUU_CCAUGGAUCGUACUUUUCG_GGCAUGGCAAAUGGCAGCGCUGAUUUACUU
....................................((((((.(((...(((((.................))))).)))))))))............. (-11.53 = -11.31 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:57:47 2006