Locus 4402

Sequence ID	3R_DroMel_CAF1
Location	11,637,714 – 11,637,819
Length	105
Max. P	0.981313

overview

Window 8

Location	11,637,714 – 11,637,819
Length	105
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	92.76
Mean single sequence MFE	-36.46
Consensus MFE	-30.84
Energy contribution	-31.72
Covariance contribution	0.88
Combinations/Pair	1.06
Mean z-score	-1.98
Structure conservation index	0.85
SVM decision value	1.88
SVM RNA-class probability	0.981313
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11637714 105 + 27905053
AACGUAUGGGACACGUCGCUGAUGGAUGUUCCGGAUGGAUGUUCCAUUAAUAUCGGAGU--AAUCCCAGUUAGCCACGGCUCGCUGUUGGCCAUGUGUCAUUCGGUU
..((.....(((((((.((..(.((((..(((((((((.....))))).....))))..--.))))((((.(((....))).)))))..)).)))))))...))... ( -37.50)
>DroSec_CAF1 18683 107 + 1
AACGUAUGGGACACGUUGCUGUUGGAUGUUCCGGAUGAAUGUUCCAUUAUUAUCGCAGUUUUAUCCCAGUUAGCCACGGCUAGCUGUUGGCCAUGUGUCAUACGGUU
..(((((..(((((((.(((...((.....))((((((((((............)))..)))))))((((((((....))))))))..))).))))))))))))... ( -36.10)
>DroSim_CAF1 15958 107 + 1
AACGUAUGGGACACGUUGCUGUUGGAUGUUCCGGAUGGAUGUUCCAUUAUUAUCGCAGUUUUAUCCCAGUUAGCCACGGCUCGCUGUUGGCCAUGUGUCAUACGGUU
..(((((..(((((((.(((.(((((((.....(((((.....)))))..)))).)))........((((.(((....))).))))..))).))))))))))))... ( -34.10)
>DroEre_CAF1 16401 105 + 1
AACGUAUGGAACACGUCGCUGAUGGAUGUUCCGGAUGGAUGUUCCAUUAUUAUCGGACU--UAUCCCAGUUAGCCACGGCUUGCUGUUGGCCAUGUGUCAUUCGGCU
..((.(((..((((((.((..(.(((((.(((((((((.....))))).....))))..--)))))((((.(((....))).)))))..)).))))))))).))... ( -36.20)
>DroYak_CAF1 19003 105 + 1
AACGUAUGGGACACGUUGCCGAUGGAUGUUCCGGAUGGAUGUUCCAUUAUUAUCGGAGU--UAUCCCGGUUAGCCACGGCUCGCUGUUGGCCAUGUGUCAUUCGGCU
..((.....(((((((.(((((.(((((((((((((((.....))))).....))))).--)))))((((.(((....))).))))))))).)))))))...))... ( -38.40)
>consensus
AACGUAUGGGACACGUUGCUGAUGGAUGUUCCGGAUGGAUGUUCCAUUAUUAUCGGAGU__UAUCCCAGUUAGCCACGGCUCGCUGUUGGCCAUGUGUCAUUCGGUU
..((.....(((((((.(((...(((((((((((((((.....))))).....)))))...)))))((((.(((....))).))))..))).)))))))...))... (-30.84 = -31.72 +   0.88)

alignment

secondary structure

dotplot

Window 9

Location	11,637,714 – 11,637,819
Length	105
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	92.76
Mean single sequence MFE	-29.24
Consensus MFE	-22.66
Energy contribution	-22.42
Covariance contribution	-0.24
Combinations/Pair	1.12
Mean z-score	-1.75
Structure conservation index	0.77
SVM decision value	0.38
SVM RNA-class probability	0.713692
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11637714 105 - 27905053
AACCGAAUGACACAUGGCCAACAGCGAGCCGUGGCUAACUGGGAUU--ACUCCGAUAUUAAUGGAACAUCCAUCCGGAACAUCCAUCAGCGACGUGUCCCAUACGUU
........(((((.(.((...(((..(((....)))..)))((((.--..((((......((((.....)))).))))..))))....)).).)))))......... ( -27.90)
>DroSec_CAF1 18683 107 - 1
AACCGUAUGACACAUGGCCAACAGCUAGCCGUGGCUAACUGGGAUAAAACUGCGAUAAUAAUGGAACAUUCAUCCGGAACAUCCAACAGCAACGUGUCCCAUACGUU
...((((((..(((((.....(((.((((....)))).))).........(((.........(((.......)))((.....))....))).)))))..)))))).. ( -28.30)
>DroSim_CAF1 15958 107 - 1
AACCGUAUGACACAUGGCCAACAGCGAGCCGUGGCUAACUGGGAUAAAACUGCGAUAAUAAUGGAACAUCCAUCCGGAACAUCCAACAGCAACGUGUCCCAUACGUU
...(((((....(((((((......).)))))).......((((((....(((.......((((.....))))..((.....))....)))...))))))))))).. ( -30.40)
>DroEre_CAF1 16401 105 - 1
AGCCGAAUGACACAUGGCCAACAGCAAGCCGUGGCUAACUGGGAUA--AGUCCGAUAAUAAUGGAACAUCCAUCCGGAACAUCCAUCAGCGACGUGUUCCAUACGUU
.((.((......((((((.........))))))........((((.--..((((......((((.....)))).))))..)))).)).))(((((((...))))))) ( -27.00)
>DroYak_CAF1 19003 105 - 1
AGCCGAAUGACACAUGGCCAACAGCGAGCCGUGGCUAACCGGGAUA--ACUCCGAUAAUAAUGGAACAUCCAUCCGGAACAUCCAUCGGCAACGUGUCCCAUACGUU
.(((((......(((((((......).))))))........((((.--..((((......((((.....)))).))))..)))).)))))(((((((...))))))) ( -32.60)
>consensus
AACCGAAUGACACAUGGCCAACAGCGAGCCGUGGCUAACUGGGAUA__ACUCCGAUAAUAAUGGAACAUCCAUCCGGAACAUCCAUCAGCAACGUGUCCCAUACGUU
........(((((.((((((...(....)..)))))).((((((......)))........((((...(((....)))...)))).)))....)))))......... (-22.66 = -22.42 +  -0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:28:13 2006