Locus 3925

Sequence ID	3R_DroMel_CAF1
Location	10,665,348 – 10,665,483
Length	135
Max. P	0.755244

overview

Window 9

Location	10,665,348 – 10,665,445
Length	97
Sequences	4
Columns	110
Reading direction	forward
Mean pairwise identity	88.58
Mean single sequence MFE	-25.81
Consensus MFE	-20.89
Energy contribution	-21.45
Covariance contribution	0.56
Combinations/Pair	1.04
Mean z-score	-1.40
Structure conservation index	0.81
SVM decision value	0.02
SVM RNA-class probability	0.543223
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10665348 97 + 27905053
UUUGGCCAACCAAGUGCCGUUGCCUGGCGUUACACGACGUCUUCCGUUUUUGGCCAACACUUCCCCU-------------CCCUCACCAAUGGACCAUUUCCUCUGGGCA
.((((((((...((.((....))))((((((....))))))........))))))))..........-------------......(((..(((.....)))..)))... ( -24.80)
>DroSec_CAF1 6990 109 + 1
UUUGGCCAACCAAGUGCCGUUGCCUGGCGUUACACGACGUCUUCCGUUUUUGGCCAACACUUCAGCUCACACUG-CACGCCCCUCUUCCAUGGACCAUUUCCUCUGGGCA
.((((((((...((.((....))))((((((....))))))........)))))))).......((.......)-)..((((.........(((.....)))...)))). ( -27.00)
>DroSim_CAF1 7060 109 + 1
UUUGGCCAACCAAGUGCCGUUGCCUGGCGUUACACGACGUCUUCCGUUUUUGGCCAACACUUCAGCUCACACUG-CACGCCCCUCUCCCAUUUACCAUUUCCUCUGGGCA
.((((((((...((.((....))))((((((....))))))........)))))))).......((.......)-)..((((.......................)))). ( -25.10)
>DroEre_CAF1 3900 110 + 1
UUUGGCCAACCAAGUGCCGUUGCCUGGCGUUACACGACGUCUUCCGUUUUUGGCCAACACUUCACCUCAGACCCCCUCUCUCCUCACCCAUGGACCAUUUCCUCUGGGCA
.((((((((...((.((....))))((((((....))))))........))))))))........((((((.........(((........)))........)))))).. ( -26.33)
>consensus
UUUGGCCAACCAAGUGCCGUUGCCUGGCGUUACACGACGUCUUCCGUUUUUGGCCAACACUUCACCUCACACUG_CACGCCCCUCACCCAUGGACCAUUUCCUCUGGGCA
.((((((((...((.((....))))((((((....))))))........)))))))).............................((((.(((.....)))..)))).. (-20.89 = -21.45 +   0.56)

alignment

secondary structure

dotplot

Window 0

Location	10,665,381 – 10,665,483
Length	102
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	88.65
Mean single sequence MFE	-36.39
Consensus MFE	-25.50
Energy contribution	-27.50
Covariance contribution	2.00
Combinations/Pair	1.00
Mean z-score	-2.15
Structure conservation index	0.70
SVM decision value	0.49
SVM RNA-class probability	0.755244
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10665381 102 - 27905053
UUCUGAAUGGCCGGCAAUGAAUUGAACAUUGUCACGCUUGCCCAGAGGAAAUGGUCCAUUGGUGAGGG-------------AGGGGAAGUGUUGGCCAAAAACGGAAGACGUCGU
(((((..((((((((((((.......)))))))((((((.(((...(((.....))).((....))..-------------.))).)))))).)))))....)))))........ ( -32.50)
>DroSec_CAF1 7023 114 - 1
UUCUGAAUGGCCGGCAAUGAAUUGAACAUUGUCACGCUUGCCCAGAGGAAAUGGUCCAUGGAAGAGGGGCGUG-CAGUGUGAGCUGAAGUGUUGGCCAAAAACGGAAGACGUCGU
(((((..(((((((((.........((((((.(((((((.((((..(((.....))).)))..)..)))))))-)))))).........)))))))))....)))))........ ( -39.97)
>DroSim_CAF1 7093 114 - 1
UUCUGAAUGGCCGGCAAUGAAUUGAACAUUGUCACGCUUGCCCAGAGGAAAUGGUAAAUGGGAGAGGGGCGUG-CAGUGUGAGCUGAAGUGUUGGCCAAAAACGGAAGACGUCGU
(((((..(((((((((.........((((((.(((((((.((((..............))))....)))))))-)))))).........)))))))))....)))))........ ( -40.41)
>DroEre_CAF1 3933 115 - 1
UUCUGAAUGGGCGGCAAUGAAUUGAACAUUGUCACGCUUGCCCAGAGGAAAUGGUCCAUGGGUGAGGAGAGAGGGGGUCUGAGGUGAAGUGUUGGCCAAAAACGGAAGACGUCGU
(((((...(((((((((((.......)))))))...((..((((..(((.....))).))))..))..........))))..(((.(.....).))).....)))))........ ( -32.70)
>consensus
UUCUGAAUGGCCGGCAAUGAAUUGAACAUUGUCACGCUUGCCCAGAGGAAAUGGUCCAUGGGAGAGGGGCGUG_CAGUGUGAGCUGAAGUGUUGGCCAAAAACGGAAGACGUCGU
(((((..((((((((((((.......))))))).(.((((((((..(((.....))).)))))))).).........................)))))....)))))........ (-25.50 = -27.50 +   2.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:35 2006