Locus 772

Sequence ID	3R_DroMel_CAF1
Location	2,677,207 – 2,677,340
Length	133
Max. P	0.967093

overview

Window 8

Location	2,677,207 – 2,677,314
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.08
Mean single sequence MFE	-29.94
Consensus MFE	-22.22
Energy contribution	-22.42
Covariance contribution	0.20
Combinations/Pair	1.08
Mean z-score	-2.68
Structure conservation index	0.74
SVM decision value	1.61
SVM RNA-class probability	0.967093
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2677207 107 + 27905053
CAUAGCAUAGCAUAGCAUCCUC-----------UCGGAUCCCAUUCCAUUCUAGAUCCAUGGAGGGUCCCC--AGCAGCAUCCAACAUGUUGCAGGCGAUUUUUCAUCAUCGCUUGCAUG
.........(((.(((......-----------..(((((.............)))))((((((((((.((--.(((((((.....))))))).)).))))))))))....))))))... ( -32.12)
>DroSec_CAF1 36630 107 + 1
CAUAGCAUAGCAUACCAUCCUC-----------UCGGAUCCCAUUCCAUUCUAGAUCCAUGGAGGGUCCCC--AGCAGCAUCCAACAUGUUGCAGGCGAUUUUUCAUCAUCGCUUGCAUG
....(((.(((...........-----------..(((((.............)))))((((((((((.((--.(((((((.....))))))).)).))))))))))....))))))... ( -32.12)
>DroSim_CAF1 29826 107 + 1
CAUAGCAUAGCAUACCAUCCUC-----------UCGGAUCCCAUUCCAUUCUAGAUCCAUGGAGGGUCCCC--AGCAGCAUCCAACAUGUUGCAGGCGAUUUUUCAUCAUCGCUUGCAUG
....(((.(((...........-----------..(((((.............)))))((((((((((.((--.(((((((.....))))))).)).))))))))))....))))))... ( -32.12)
>DroYak_CAF1 37111 102 + 1
CAUAGCAUA-----CCAUCCGC-----------GCAGAUCCCAUUCCAUUCUAGAUCCAUGGAGGGUCCCC--AACAGCAUCCAACAUGUUGCAGGCGAUUUUUCAUCAUCGCUUGCAUG
...(((((.-----......((-----------...(((((...(((((.........))))))))))...--....)).......)))))(((((((((........)))))))))... ( -24.34)
>DroAna_CAF1 24867 117 + 1
CAGAGCAACCCGUACCAUCCUCCUCCCUCCAUCCCAGAUUCCAU---AUCCCAGAUCCAUGGAGGGUCCCCUCGACAGCAUCCAACAUGUUGCAGGCGAUUUUUCAUCAUCGCUUGCAUG
....((...................(((((((....((((....---......)))).)))))))(((.....))).))...........((((((((((........)))))))))).. ( -29.00)
>consensus
CAUAGCAUAGCAUACCAUCCUC___________UCGGAUCCCAUUCCAUUCUAGAUCCAUGGAGGGUCCCC__AGCAGCAUCCAACAUGUUGCAGGCGAUUUUUCAUCAUCGCUUGCAUG
...(((((...........................(((((.............))))).((((..((.......))....))))..)))))(((((((((........)))))))))... (-22.22 = -22.42 +   0.20)

alignment

secondary structure

dotplot

Window 9

Location	2,677,236 – 2,677,340
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.95
Mean single sequence MFE	-30.68
Consensus MFE	-25.20
Energy contribution	-25.16
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.91
Structure conservation index	0.82
SVM decision value	1.23
SVM RNA-class probability	0.934050
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2677236 104 + 27905053
CCAUUCCAUUCUAGAUCCAUGGAGGGUCCCC--AGCAGCAUCCAACAUGUUGCAGGCGAUUUUUCAUCAUCGCUUGCAUGUUG-----CCUCCGA--------UUGUAAAUGUUG-CCCC
......((((...((((...(((((.....(--((((((((.....))))((((((((((........)))))))))))))))-----)))))))--------))...))))...-.... ( -29.20)
>DroSec_CAF1 36659 104 + 1
CCAUUCCAUUCUAGAUCCAUGGAGGGUCCCC--AGCAGCAUCCAACAUGUUGCAGGCGAUUUUUCAUCAUCGCUUGCAUGUUG-----CCUCCGA--------UUGUAAAUGUUG-CCCC
......((((...((((...(((((.....(--((((((((.....))))((((((((((........)))))))))))))))-----)))))))--------))...))))...-.... ( -29.20)
>DroSim_CAF1 29855 104 + 1
CCAUUCCAUUCUAGAUCCAUGGAGGGUCCCC--AGCAGCAUCCAACAUGUUGCAGGCGAUUUUUCAUCAUCGCUUGCAUGUUG-----CCUCCGA--------UUGUAAAUGUUG-CCCC
......((((...((((...(((((.....(--((((((((.....))))((((((((((........)))))))))))))))-----)))))))--------))...))))...-.... ( -29.20)
>DroYak_CAF1 37135 104 + 1
CCAUUCCAUUCUAGAUCCAUGGAGGGUCCCC--AACAGCAUCCAACAUGUUGCAGGCGAUUUUUCAUCAUCGCUUGCAUGUUG-----CCUCCGA--------GUGUAAAUGUUG-CCCC
.((((.(((((..(((((.....)))))..(--((((((((.....))))((((((((((........)))))))))))))))-----.....))--------)))..))))...-.... ( -29.10)
>DroAna_CAF1 24907 117 + 1
CCAU---AUCCCAGAUCCAUGGAGGGUCCCCUCGACAGCAUCCAACAUGUUGCAGGCGAUUUUUCAUCAUCGCUUGCAUGUUGUUACCCCGCCGAUGUGGAUAUUGAAGUUGUUGGUGCC
....---......(((((.....)))))...((((((((.(((((((...((((((((((........))))))))))))))).....((((....)))).....)).)))))))).... ( -36.70)
>consensus
CCAUUCCAUUCUAGAUCCAUGGAGGGUCCCC__AGCAGCAUCCAACAUGUUGCAGGCGAUUUUUCAUCAUCGCUUGCAUGUUG_____CCUCCGA________UUGUAAAUGUUG_CCCC
...................((((((((.......))......(((((...((((((((((........))))))))))))))).....)))))).......................... (-25.20 = -25.16 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:42 2006