Locus 678

Sequence ID	X_DroMel_CAF1
Location	1,879,245 – 1,879,385
Length	140
Max. P	0.992719

overview

Window 9

Location	1,879,245 – 1,879,345
Length	100
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	90.19
Mean single sequence MFE	-26.04
Consensus MFE	-21.40
Energy contribution	-21.56
Covariance contribution	0.16
Combinations/Pair	1.05
Mean z-score	-2.45
Structure conservation index	0.82
SVM decision value	2.35
SVM RNA-class probability	0.992719
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1879245 100 - 22224390
CUGCGGGAUCCUGUCUUCCCUUUUCAGUUCAGCAGCAGCCUAAGGUUGGAUUAUAAUCUUGGCCUCAAUU-UU---UUUGUGCUGCAUUCUCUCUUAAAUUACU
....((((........))))...........(((((((((.(((((((.....))))))))))..(((..-..---.))))))))).................. ( -25.20)
>DroSec_CAF1 4015 100 - 1
CUGCGGGAUCCUGUCUUCCCU-UUCAGUUCAGCAGCAGCCUAAGGUUGGAUUAUAAUCUUGGCCAAAAUUAUU---UUUGUGCUGCAUUCUUUCUUAAAUUACU
(((.((((........)))).-..)))....(((((((((.(((((((.....))))))))))(((((....)---)))))))))).................. ( -27.80)
>DroSim_CAF1 5418 100 - 1
CUGCGGGAUCCUGUCUUCCCU-UUCAGUUCAGCAGCAGCCUAAGGUUGGAUUAUAAUCUUGGCCAAAAUUCUU---UUUGUGCUGCAUUCUCUCUUAAAUUACU
(((.((((........)))).-..)))....(((((((((.(((((((.....))))))))))(((((....)---)))))))))).................. ( -27.80)
>DroEre_CAF1 4070 100 - 1
CUCCGGGAUCCUGGCUUCCCU-UUCAGUUCAGCAGCAGCAUAAGGUUGGAUUAUGAUCUUGGCCACAAUUUCUUGUUUUGUGCUGCAUU---UCUUAAAGUAGU
....((((........)))).-............((((((((((((..(.........)..)))((((....)))).)))))))))...---............ ( -24.70)
>DroYak_CAF1 4653 101 - 1
CUCCGGGAUCCUGGCUUCCCUUUUCAGUUCAGCAGCAGCCUAAGGUUCGUUUAUGAUCUUGGCCACAAUUUCU---UUUGUGCUGCAUUCUCUCUUAAAGUAGU
....((((........))))...........(((((.(((.((((((.......))))))))).((((.....---.))))))))).................. ( -24.70)
>consensus
CUGCGGGAUCCUGUCUUCCCU_UUCAGUUCAGCAGCAGCCUAAGGUUGGAUUAUAAUCUUGGCCACAAUUUUU___UUUGUGCUGCAUUCUCUCUUAAAUUACU
....((((........))))...........(((((((((.(((((((.....)))))))))).................)))))).................. (-21.40 = -21.56 +   0.16)

alignment

secondary structure

dotplot

Window 0

Location	1,879,271 – 1,879,385
Length	114
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	91.44
Mean single sequence MFE	-33.68
Consensus MFE	-30.72
Energy contribution	-30.80
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.26
Structure conservation index	0.91
SVM decision value	0.43
SVM RNA-class probability	0.735056
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1879271 114 - 22224390
AAAGCUCCUGGCAUGAUUGGAGCUCAUGCAAAAACUGGGGCUGCGGGAUCCUGUCUUCCCUUUUCAGUUCAGCAGCAGCCUAAGGUUGGAUUAUAAUCUUGGCCUCAAUU-UU---UU
...(((.(((((((((.......))))))...(((((..(....((((........)))).)..)))))))).))).(((.(((((((.....)))))))))).......-..---.. ( -34.80)
>DroSec_CAF1 4041 113 - 1
AAAGCUCCUGGCAUGAUUAGGACUCAUGCAA-AACUGGGGCUGCGGGAUCCUGUCUUCCCU-UUCAGUUCAGCAGCAGCCUAAGGUUGGAUUAUAAUCUUGGCCAAAAUUAUU---UU
...(((.(((((((((.......))))))..-(((((..(....((((........)))))-..)))))))).))).(((.(((((((.....))))))))))..........---.. ( -34.70)
>DroSim_CAF1 5444 113 - 1
AAAGCUCCUGGCAUGAUUAGGACUCAUGCAA-AACUGGGGCUGCGGGAUCCUGUCUUCCCU-UUCAGUUCAGCAGCAGCCUAAGGUUGGAUUAUAAUCUUGGCCAAAAUUCUU---UU
...(((.(((((((((.......))))))..-(((((..(....((((........)))))-..)))))))).))).(((.(((((((.....))))))))))..........---.. ( -34.70)
>DroEre_CAF1 4093 116 - 1
AAAGCUCCUGGGAUGAUUGGGACUCAUGCAA-AACUGGGGCUCCGGGAUCCUGGCUUCCCU-UUCAGUUCAGCAGCAGCAUAAGGUUGGAUUAUGAUCUUGGCCACAAUUUCUUGUUU
...(((.(((((.(((..((((((((.....-...))))...((((....))))..)))).-.))).))))).))).((.((((((((.....))))))))))............... ( -32.50)
>DroYak_CAF1 4679 115 - 1
AAAGCUCCUGGGAUGAUUGGGACUCAUGCAAAAACUGGGGCUCCGGGAUCCUGGCUUCCCUUUUCAGUUCAGCAGCAGCCUAAGGUUCGUUUAUGAUCUUGGCCACAAUUUCU---UU
...(((.(((((.(((..((((((((.(......)))))...((((....))))..))))...))).))))).))).(((.((((((.......)))))))))..........---.. ( -31.70)
>consensus
AAAGCUCCUGGCAUGAUUGGGACUCAUGCAA_AACUGGGGCUGCGGGAUCCUGUCUUCCCU_UUCAGUUCAGCAGCAGCCUAAGGUUGGAUUAUAAUCUUGGCCACAAUUUUU___UU
...(((.(((((((((.......)))))).......((((..((((....))))..)))).........))).))).(((.(((((((.....))))))))))............... (-30.72 = -30.80 +   0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:56 2006