Locus 7546

Sequence ID	3L_DroMel_CAF1
Location	20,252,715 – 20,252,835
Length	120
Max. P	0.986787

overview

Window 2

Location	20,252,715 – 20,252,835
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	95.14
Mean single sequence MFE	-35.25
Consensus MFE	-31.52
Energy contribution	-31.65
Covariance contribution	0.13
Combinations/Pair	1.07
Mean z-score	-2.49
Structure conservation index	0.89
SVM decision value	1.53
SVM RNA-class probability	0.961474
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20252715 120 + 23771897
ACCACUUCCACCAUCGAAGUAGCCACCCUGCAGGCCAUAUACACCGGCAAGGGGUAUCCCAUCAAGAACAACUACCGCGAUGCUAUUCAAAACUACAAUGUCCAGCCGAUGGAAGUGGAC
.((((((((..(((((..((((..(((((....(((.........)))..))))).((.......))....))))..))))).................(((.....))))))))))).. ( -34.20)
>DroSec_CAF1 5019 120 + 1
ACCACUUCCACCAUCGAAGUAGCCACCCUGCAGGCCAUAUACACCGGCAAGGGGUAUCCCAUCAAGAACAACUACCGCGAUGCUAUUCAGAACUACAAUGUGCAGCCGAUGGAAGUGGAC
.(((((((((.(((((..((((..(((((....(((.........)))..))))).((.......))....))))..))))).......(.((......)).)......))))))))).. ( -35.00)
>DroSim_CAF1 4995 120 + 1
ACCACUUCCACCAUCGAAGUAGCCACCCUGCAGGCCAUAUACACCGGCAAGGGGUAUCCCAUCAAGAACAACUACCGCGAUGCUAUUCAGAACUACAAUGUGCAGCCGAUGGAAGUGGAC
.(((((((((.(((((..((((..(((((....(((.........)))..))))).((.......))....))))..))))).......(.((......)).)......))))))))).. ( -35.00)
>DroYak_CAF1 5537 120 + 1
ACCACUUCCACCAUCGAAGUGGCCACCCUGCAGGCCAUUUACACCAGCAAGGGGUAUCACAUCAAGGACAACUACCGCGUUGCCAUUCAGAACUACAAUGUACAGCCAAAGGAAGUGGAC
.(((((((((((....((((((((........))))))))...((.....)))))..........((.((((......))))))..........................)))))))).. ( -36.80)
>consensus
ACCACUUCCACCAUCGAAGUAGCCACCCUGCAGGCCAUAUACACCGGCAAGGGGUAUCCCAUCAAGAACAACUACCGCGAUGCUAUUCAGAACUACAAUGUGCAGCCGAUGGAAGUGGAC
.((((((((..(((((..((((..(((((....(((.........)))..))))).((.......))....))))..))))).........((......)).........)))))))).. (-31.52 = -31.65 +   0.13)

alignment

secondary structure

dotplot

Window 3

Location	20,252,715 – 20,252,835
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	95.14
Mean single sequence MFE	-48.10
Consensus MFE	-44.16
Energy contribution	-44.60
Covariance contribution	0.44
Combinations/Pair	1.07
Mean z-score	-2.95
Structure conservation index	0.92
SVM decision value	2.05
SVM RNA-class probability	0.986787
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20252715 120 - 23771897
GUCCACUUCCAUCGGCUGGACAUUGUAGUUUUGAAUAGCAUCGCGGUAGUUGUUCUUGAUGGGAUACCCCUUGCCGGUGUAUAUGGCCUGCAGGGUGGCUACUUCGAUGGUGGAAGUGGU
..(((((((((((.((((..((.........))..))))((((.(((((.((((((....))))))((((((((.(((.......))).)))))).))))))).))))))))))))))). ( -50.10)
>DroSec_CAF1 5019 120 - 1
GUCCACUUCCAUCGGCUGCACAUUGUAGUUCUGAAUAGCAUCGCGGUAGUUGUUCUUGAUGGGAUACCCCUUGCCGGUGUAUAUGGCCUGCAGGGUGGCUACUUCGAUGGUGGAAGUGGU
..(((((((((((((((((.....)))))).........((((.(((((.((((((....))))))((((((((.(((.......))).)))))).))))))).))))))))))))))). ( -50.70)
>DroSim_CAF1 4995 120 - 1
GUCCACUUCCAUCGGCUGCACAUUGUAGUUCUGAAUAGCAUCGCGGUAGUUGUUCUUGAUGGGAUACCCCUUGCCGGUGUAUAUGGCCUGCAGGGUGGCUACUUCGAUGGUGGAAGUGGU
..(((((((((((((((((.....)))))).........((((.(((((.((((((....))))))((((((((.(((.......))).)))))).))))))).))))))))))))))). ( -50.70)
>DroYak_CAF1 5537 120 - 1
GUCCACUUCCUUUGGCUGUACAUUGUAGUUCUGAAUGGCAACGCGGUAGUUGUCCUUGAUGUGAUACCCCUUGCUGGUGUAAAUGGCCUGCAGGGUGGCCACUUCGAUGGUGGAAGUGGU
..((((((((...((((.(((((((.((........((((((......))))))))))))))).....((((((.(((.......))).)))))).))))(((.....))))))))))). ( -40.90)
>consensus
GUCCACUUCCAUCGGCUGCACAUUGUAGUUCUGAAUAGCAUCGCGGUAGUUGUUCUUGAUGGGAUACCCCUUGCCGGUGUAUAUGGCCUGCAGGGUGGCUACUUCGAUGGUGGAAGUGGU
..(((((((((((.((((..((.........))..))))((((.(((((.((((((....))))))((((((((.(((.......))).)))))).))))))).))))))))))))))). (-44.16 = -44.60 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:53 2006