Locus 1154

Sequence ID 3R_DroMel_CAF1
Location 3,484,442 – 3,484,542
Length 100
Max. P 0.978589
window1894 window1895

overview

Window 4

Location 3,484,442 – 3,484,542
Length 100
Sequences 4
Columns 105
Reading direction forward
Mean pairwise identity 85.69
Mean single sequence MFE -21.83
Consensus MFE -16.88
Energy contribution -16.50
Covariance contribution -0.38
Combinations/Pair 1.16
Mean z-score -1.97
Structure conservation index 0.77
SVM decision value 0.83
SVM RNA-class probability 0.861285
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3484442 100 + 27905053
GGC-----CAAAUAGCCCGUGAAAAUACAUUUCCAAAAGAAAUAAUGUUGUCUUCGUAUACGAAAUUCCACGGCUAUUUGGGUUAAUUAAGAAUCGAAAAUGCUU
..(-----(((((((((.(((.......(((((.....))))).........((((....))))....)))))))))))))........................ ( -23.20)
>DroSec_CAF1 82032 100 + 1
GGC-----CAAAUAGCCCGUGAAAAUACAUUACCAAAGGAAAUAAUGUUGUCCUCGUAUAUAAAAUUCCACGGCUAUUUGGGUUAAUUAAGAACCAAAAAUGCUC
(((-----(((((((((.(((.........(((...((((.(......).)))).)))..........))))))))))))((((.......))))......))). ( -21.91)
>DroSim_CAF1 105830 100 + 1
GGC-----CAAAUAGCCCGUGAAAAUACAUUUCCAAAAGAAAUAAUGUUGUCCUCGUAUAUGAAAUUCCACGGCUAUUUGGGUUAAUUAAGAACCAAAAAUGCUC
(((-----(((((((((.(((.......(((((.....))))).(((.......)))...........))))))))))))((((.......))))......))). ( -20.60)
>DroYak_CAF1 146728 101 + 1
GGCAAAUGCAAAUAGCUCGUGAAAAUACAUAUUCGAACGAAAUAAUGUUGUUCUCAUAUACGAAGUACCACGGCUAUUUGGGUUAAUUAAAAAUCGAA--UCG--
....(((.((((((((.((((....(((......((((((.......))))))((......)).))).)))))))))))).)))..............--...-- ( -21.60)
>consensus
GGC_____CAAAUAGCCCGUGAAAAUACAUUUCCAAAAGAAAUAAUGUUGUCCUCGUAUACGAAAUUCCACGGCUAUUUGGGUUAAUUAAGAACCAAAAAUGCUC
........((((((((.((((.......(((((.....)))))....((((........)))).....))))))))))))((((.......)))).......... (-16.88 = -16.50 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 3,484,442 – 3,484,542
Length 100
Sequences 4
Columns 105
Reading direction reverse
Mean pairwise identity 85.69
Mean single sequence MFE -26.15
Consensus MFE -19.50
Energy contribution -18.87
Covariance contribution -0.63
Combinations/Pair 1.26
Mean z-score -2.82
Structure conservation index 0.75
SVM decision value 1.82
SVM RNA-class probability 0.978589
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3484442 100 - 27905053
AAGCAUUUUCGAUUCUUAAUUAACCCAAAUAGCCGUGGAAUUUCGUAUACGAAGACAACAUUAUUUCUUUUGGAAAUGUAUUUUCACGGGCUAUUUG-----GCC
........................(((((((((((((((((((((....))))).......((((((.....))))))...)))))).)))))))))-----).. ( -27.40)
>DroSec_CAF1 82032 100 - 1
GAGCAUUUUUGGUUCUUAAUUAACCCAAAUAGCCGUGGAAUUUUAUAUACGAGGACAACAUUAUUUCCUUUGGUAAUGUAUUUUCACGGGCUAUUUG-----GCC
((((.......)))).........((((((((((((((((...((((((((((((..........)))))..)).))))).)))))).)))))))))-----).. ( -29.20)
>DroSim_CAF1 105830 100 - 1
GAGCAUUUUUGGUUCUUAAUUAACCCAAAUAGCCGUGGAAUUUCAUAUACGAGGACAACAUUAUUUCUUUUGGAAAUGUAUUUUCACGGGCUAUUUG-----GCC
((((.......)))).........((((((((((((((((((((......)))).......((((((.....))))))...)))))).)))))))))-----).. ( -26.60)
>DroYak_CAF1 146728 101 - 1
--CGA--UUCGAUUUUUAAUUAACCCAAAUAGCCGUGGUACUUCGUAUAUGAGAACAACAUUAUUUCGUUCGAAUAUGUAUUUUCACGAGCUAUUUGCAUUUGCC
--...--..................(((((((((((((.....(((((....((((...........))))..))))).....))))).))))))))........ ( -21.40)
>consensus
GAGCAUUUUCGAUUCUUAAUUAACCCAAAUAGCCGUGGAAUUUCAUAUACGAGGACAACAUUAUUUCUUUUGGAAAUGUAUUUUCACGGGCUAUUUG_____GCC
.........................(((((((((((((((...(((...(((((.............)))))...)))...))))))).))))))))........ (-19.50 = -18.87 +  -0.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:23 2006