Locus 2228

Sequence ID	2L_DroMel_CAF1
Location	6,056,255 – 6,056,411
Length	156
Max. P	0.825841

overview

Window 0

Location	6,056,255 – 6,056,371
Length	116
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.44
Mean single sequence MFE	-34.20
Consensus MFE	-25.71
Energy contribution	-25.77
Covariance contribution	0.06
Combinations/Pair	1.13
Mean z-score	-1.44
Structure conservation index	0.75
SVM decision value	-0.05
SVM RNA-class probability	0.507493
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6056255 116 - 22407834
AGAGUGCAUGGGGUAAGGGUCCUUUGUGGGCUAUUCCCAUGCGGUGAUUCAUAUCUCUUGCAUGGCAUGGCAGUAAAUUUUGCUUCAUUAAAAUCGGAUGACUGUAGAAUUGGGCA----
.(.(((((.((((((.(((((((.((((((.....)))))).)).))))).)))))).)))))..)...((....((((((((.(((((.......)))))..))))))))..)).---- ( -37.10)
>DroSec_CAF1 18060 120 - 1
AGAGUGCAUGGGGUAAAGGUCCUUUGUGGGCUAUUCCCAUGCGGUGAUUCAUAUCUCUUGCAUGGCAUGGCCGUAAAUUUUGCUUCAUUAAAAUCGGAUGACUGUAGAAUUGGGCAGUAU
((((.((((((((....(((((.....)))))..))))))))((....))....))))((((((((...))))).((((((((.(((((.......)))))..))))))))..))).... ( -37.60)
>DroSim_CAF1 19122 120 - 1
AGAGUGCAUGGGGUAAAGGUCCUUUGUGGGCUAUUCCCAUGCGGUGAUUCAUAUCUCUUGCAUGGCAUGGCAGUAAAUUUUGCUUCAUUAAAAUCGGAUGACUGUAGAAUUGGGCAGUAU
.(.(((((.((((((..((((((.((((((.....)))))).)).))))..)))))).)))))..)...((....((((((((.(((((.......)))))..))))))))..))..... ( -34.40)
>DroEre_CAF1 19280 119 - 1
AGAGUACAUGGG-AAAGGGUCCUUUGUGGGCUAUUUCUAUGCGGUGAUUCAUAUGAUUUGCAUGUUAUGGCAGUACAUUUUCCUACAUACAAAUCGGAUAACUGUUUAAUUGGGUAGUAU
...(((((((((-((..(((((.....))))).)))))))(((((.((((....((((((.((((...((.((.....)).)).)))).)))))))))).)))))...........)))) ( -27.70)
>consensus
AGAGUGCAUGGGGUAAAGGUCCUUUGUGGGCUAUUCCCAUGCGGUGAUUCAUAUCUCUUGCAUGGCAUGGCAGUAAAUUUUGCUUCAUUAAAAUCGGAUGACUGUAGAAUUGGGCAGUAU
....(((((((((....(((((.....)))))..))))))(((((.((((........(((...))).(((((......)))))...........)))).)))))........))).... (-25.71 = -25.77 +   0.06)

alignment

secondary structure

dotplot

Window 1

Location	6,056,291 – 6,056,411
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.07
Mean single sequence MFE	-35.36
Consensus MFE	-27.80
Energy contribution	-29.36
Covariance contribution	1.56
Combinations/Pair	1.17
Mean z-score	-1.82
Structure conservation index	0.79
SVM decision value	0.70
SVM RNA-class probability	0.825841
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6056291 120 - 22407834
CAAUUAGUCGCAGAUUAAAAGUGUGUGCGGUGUUCAUGAUAGAGUGCAUGGGGUAAGGGUCCUUUGUGGGCUAUUCCCAUGCGGUGAUUCAUAUCUCUUGCAUGGCAUGGCAGUAAAUUU
...((((((...)))))).......(((.((((.((((..((((.((((((((....(((((.....)))))..))))))))((....))....))))..)))))))).)))........ ( -39.20)
>DroSec_CAF1 18100 120 - 1
CAAUUAGUCGCAGAUUAAAAGUGUGUACCGUGUUCAUGAUAGAGUGCAUGGGGUAAAGGUCCUUUGUGGGCUAUUCCCAUGCGGUGAUUCAUAUCUCUUGCAUGGCAUGGCCGUAAAUUU
.........(((.((.....)).))).((((((.((((..((((.((((((((....(((((.....)))))..))))))))((....))....))))..)))))))))).......... ( -37.10)
>DroSim_CAF1 19162 120 - 1
CAAUUAGUCGCAGAUUAAAAGUGUGUACCGUGUUCAUGAUAGAGUGCAUGGGGUAAAGGUCCUUUGUGGGCUAUUCCCAUGCGGUGAUUCAUAUCUCUUGCAUGGCAUGGCAGUAAAUUU
......((((((.((.....)).))).((((((....((((((((((((((((....(((((.....)))))..))))))))....)))).))))....))))))...)))......... ( -37.20)
>DroEre_CAF1 19320 119 - 1
CAAUUAGUCGCAGAUUAAAUGUGUACACCGUGUUCAUGAUAGAGUACAUGGG-AAAGGGUCCUUUGUGGGCUAUUUCUAUGCGGUGAUUCAUAUGAUUUGCAUGUUAUGGCAGUACAUUU
.........((((((((.(((.((.((((((((....(((((..((((.(((-(.....)))).))))..)))))...)))))))))).))).)))))))).(((....)))........ ( -36.20)
>DroYak_CAF1 19299 113 - 1
CAAUUAGUCGCAGAUUAAAAGUGUGUACCGUGUUUAUAAUAGAGUAUGUGGG-AAGGGGUCCUUUGUUGGCUAUUCCUAUGCGGUAAUCCAUAUGUUUUGCAUGGUAUGGCAGU------
......((((((.((.....)).)))(((((((....((((..((..(((((-((..((.((......)))).)))))))))((....))...))))..)))))))..)))...------ ( -27.10)
>consensus
CAAUUAGUCGCAGAUUAAAAGUGUGUACCGUGUUCAUGAUAGAGUGCAUGGGGUAAGGGUCCUUUGUGGGCUAUUCCCAUGCGGUGAUUCAUAUCUCUUGCAUGGCAUGGCAGUAAAUUU
......((((((.((.....)).)))(((((((....((((((((((((((((....(((((.....)))))..))))))))....)))).))))....)))))))..)))......... (-27.80 = -29.36 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:38 2006