Locus 1709

Sequence ID	3L_DroMel_CAF1
Location	4,979,925 – 4,980,026
Length	101
Max. P	0.993233

overview

Window 7

Location	4,979,925 – 4,980,026
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	70.87
Mean single sequence MFE	-19.08
Consensus MFE	-9.93
Energy contribution	-11.90
Covariance contribution	1.97
Combinations/Pair	1.17
Mean z-score	-1.78
Structure conservation index	0.52
SVM decision value	0.95
SVM RNA-class probability	0.887183
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4979925 101 + 23771897
UGAGAUAUUCUCCCUUCGAA----AUUACCUUUUACAGCCCGAUGAACUUCAAGAUAAAGUUCAACAUUUUAUGGGAGCCACAUCGCUCCCCCAAAUCCGUAAAU---------------
.(((.....)))........----.......(((((.....(.(((((((.......))))))).).......((((((......))))))........))))).--------------- ( -21.40)
>DroPse_CAF1 255408 111 + 1
AAACUCUUUCCCCGCCCGAACUAGACUUCCCUCAAAGAUCCCAUAAA--UCCAUAAAGAAGCCAAUAUU-CGGGGCAGG--CAUUUCUCCCCCUG----GAAAGUCUCACCUUUGUCUGG
...........(((..((((..((((((.((................--........(((.......))-)((((.(((--....))).)))).)----).))))))....))))..))) ( -21.00)
>DroSec_CAF1 200595 101 + 1
UGGGAUAUUCUCCCUUCGAA----AUUACAUUUUACAGCCCGAUGAACUUCAAGAUAAAGUUCAACAUUUUAUGGGAGCCACAUCGCUCCCCCAAAUCCGUAAAU---------------
.((((.....))))......----.......(((((.....(.(((((((.......))))))).).......((((((......))))))........))))).--------------- ( -24.50)
>DroSim_CAF1 220018 101 + 1
UGAGAUAUUCUCCCUUCGAA----AUUACAUUUUACAGCCCGAUGAACUUCAAGAUAAAGUUCAACAUUUUAUGGGAGCCACAUCGCUCCCCCAAAUCCGUAAAU---------------
.(((.....)))........----.......(((((.....(.(((((((.......))))))).).......((((((......))))))........))))).--------------- ( -21.40)
>DroEre_CAF1 203764 81 + 1
-GAGAUAUU-----------------------UUACAGCCCGACGAACUUCAAGAUAAAGUUCAACAUUUUAUGGGUGCCACAUCGCUCCCCCAAAUCCGUAAAU---------------
-.......(-----------------------((((........((((((.......))))))..........(((.((......)).)))........))))).--------------- ( -14.40)
>DroYak_CAF1 207857 101 + 1
UGAGAUAUUCUCCCCUCGAA----AAUUCCUUUAACAGCCCGAUGAACUUCAAGAUAAAGUUCAACAUUUUAUGGCAGCCACAUUGCUCCCCCAAAUCCGUAAAU---------------
.(((.....)))........----.................(.(((((((.......))))))).)..(((((((.(((......))).........))))))).--------------- ( -11.80)
>consensus
UGAGAUAUUCUCCCUUCGAA____AUUACCUUUUACAGCCCGAUGAACUUCAAGAUAAAGUUCAACAUUUUAUGGGAGCCACAUCGCUCCCCCAAAUCCGUAAAU_______________
...............................(((((.......(((((((.......))))))).........((((((......))))))........)))))................ ( -9.93 = -11.90 +   1.97)

alignment

secondary structure

dotplot

Window 8

Location	4,979,925 – 4,980,026
Length	101
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	70.87
Mean single sequence MFE	-29.97
Consensus MFE	-16.17
Energy contribution	-18.37
Covariance contribution	2.20
Combinations/Pair	1.22
Mean z-score	-2.39
Structure conservation index	0.54
SVM decision value	2.38
SVM RNA-class probability	0.993233
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4979925 101 - 23771897
---------------AUUUACGGAUUUGGGGGAGCGAUGUGGCUCCCAUAAAAUGUUGAACUUUAUCUUGAAGUUCAUCGGGCUGUAAAAGGUAAU----UUCGAAGGGAGAAUAUCUCA
---------------.(((((((.(((((((((((......)))))).........((((((((.....))))))))))))))))))))(((((.(----(((.....)))).))))).. ( -32.30)
>DroPse_CAF1 255408 111 - 1
CCAGACAAAGGUGAGACUUUC----CAGGGGGAGAAAUG--CCUGCCCCG-AAUAUUGGCUUCUUUAUGGA--UUUAUGGGAUCUUUGAGGGAAGUCUAGUUCGGGCGGGGAAAGAGUUU
................(((((----(..(((.(....).--)))((((.(-(((...(((((((((..(((--((.....)))))...)))))))))..))))))))..))))))..... ( -38.10)
>DroSec_CAF1 200595 101 - 1
---------------AUUUACGGAUUUGGGGGAGCGAUGUGGCUCCCAUAAAAUGUUGAACUUUAUCUUGAAGUUCAUCGGGCUGUAAAAUGUAAU----UUCGAAGGGAGAAUAUCCCA
---------------.(((((((.(((((((((((......)))))).........((((((((.....)))))))))))))))))))).......----......((((.....)))). ( -33.90)
>DroSim_CAF1 220018 101 - 1
---------------AUUUACGGAUUUGGGGGAGCGAUGUGGCUCCCAUAAAAUGUUGAACUUUAUCUUGAAGUUCAUCGGGCUGUAAAAUGUAAU----UUCGAAGGGAGAAUAUCUCA
---------------.(((((((.(((((((((((......)))))).........((((((((.....)))))))))))))))))))).......----......((((.....)))). ( -30.90)
>DroEre_CAF1 203764 81 - 1
---------------AUUUACGGAUUUGGGGGAGCGAUGUGGCACCCAUAAAAUGUUGAACUUUAUCUUGAAGUUCGUCGGGCUGUAA-----------------------AAUAUCUC-
---------------.(((((((.((((((((.((......)).)))..........(((((((.....))))))).)))))))))))-----------------------).......- ( -21.80)
>DroYak_CAF1 207857 101 - 1
---------------AUUUACGGAUUUGGGGGAGCAAUGUGGCUGCCAUAAAAUGUUGAACUUUAUCUUGAAGUUCAUCGGGCUGUUAAAGGAAUU----UUCGAGGGGAGAAUAUCUCA
---------------....((((.(((((((.(((......))).)).........((((((((.....)))))))))))))))))...(((.(((----(((.....)))))).))).. ( -22.80)
>consensus
_______________AUUUACGGAUUUGGGGGAGCGAUGUGGCUCCCAUAAAAUGUUGAACUUUAUCUUGAAGUUCAUCGGGCUGUAAAAGGUAAU____UUCGAAGGGAGAAUAUCUCA
................(((((((.(((((((((((......)))))).........(((((((((...)))))))))))))))))))))............................... (-16.17 = -18.37 +   2.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:14 2006