Locus 1218

Sequence ID 3L_DroMel_CAF1
Location 3,463,469 – 3,463,559
Length 90
Max. P 0.709960
window1915 window1916

overview

Window 5

Location 3,463,469 – 3,463,559
Length 90
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 87.78
Mean single sequence MFE -22.51
Consensus MFE -15.35
Energy contribution -17.35
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -2.02
Structure conservation index 0.68
SVM decision value 0.37
SVM RNA-class probability 0.709960
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3463469 90 + 23771897
CAUUUUUAUGUAUUUGACAUUUUGCGUUAUGCGUUCAAAAUGCCAUCAAAAUGUGCAUAAAUUUCGCGUGUCUUUCUCGGUACGUGUGU---G----
....((((((((((((((((((((((.....))..)))))))...))))...)))))))))...(((((..(......)..)))))...---.---- ( -20.60)
>DroSec_CAF1 10657 94 + 1
CAUUUUUAUGUAUUUGACAUUUUGCGUUAUGCGUUCAAAAUGUCAUCAAAAUGAGCAUAAAUUUCGAGUGUCUUGCUCGGUACGUGUGU---GUGUG
.....((((.....((((((((((((.....))..)))))))))).....))))(((((....((((((.....))))))....)))))---..... ( -24.30)
>DroSim_CAF1 10743 94 + 1
CAUUUUUAUGUAUUUGACAUUUUGCGUUAUGCGUUCAAAAUGUCAUCAAAAUGUGCAUAAAUUUCGCGUGUCUUGCUCGGUACGUGUGU---GUGUG
....(((((((((.((((((((((((.....))..)))))))))).......)))))))))...(((((..(......)..)))))...---..... ( -24.50)
>DroYak_CAF1 11052 96 + 1
CAUUUUUAUGUAUUUGACAUUUUGCGUUAUGCGUUCAAAAUGUCAUCAAAAUGUGCAUAAAUUUUGCGCGUCUUUUUUUUUU-UUUUGUGGGGCACG
....(((((((((.((((((((((((.....))..)))))))))).......))))))))).....((.(((((........-......))))).)) ( -20.64)
>consensus
CAUUUUUAUGUAUUUGACAUUUUGCGUUAUGCGUUCAAAAUGUCAUCAAAAUGUGCAUAAAUUUCGCGUGUCUUGCUCGGUACGUGUGU___GUGUG
....(((((((((.((((((((((((.....))..)))))))))).......)))))))))...(((((..(......)..)))))........... (-15.35 = -17.35 +   2.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,463,469 – 3,463,559
Length 90
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 87.78
Mean single sequence MFE -14.44
Consensus MFE -12.07
Energy contribution -11.70
Covariance contribution -0.37
Combinations/Pair 1.11
Mean z-score -1.43
Structure conservation index 0.84
SVM decision value 0.09
SVM RNA-class probability 0.577776
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3463469 90 - 23771897
----C---ACACACGUACCGAGAAAGACACGCGAAAUUUAUGCACAUUUUGAUGGCAUUUUGAACGCAUAACGCAAAAUGUCAAAUACAUAAAAAUG
----.---...(.(((..(......)..))).)...((((((((.....)).((((((((((..((.....))))))))))))....)))))).... ( -12.60)
>DroSec_CAF1 10657 94 - 1
CACAC---ACACACGUACCGAGCAAGACACUCGAAAUUUAUGCUCAUUUUGAUGACAUUUUGAACGCAUAACGCAAAAUGUCAAAUACAUAAAAAUG
.....---......(((..(((((.((..........)).))))).......((((((((((..((.....))))))))))))..)))......... ( -16.90)
>DroSim_CAF1 10743 94 - 1
CACAC---ACACACGUACCGAGCAAGACACGCGAAAUUUAUGCACAUUUUGAUGACAUUUUGAACGCAUAACGCAAAAUGUCAAAUACAUAAAAAUG
.....---......(((.....(((((...(((.......)))...))))).((((((((((..((.....))))))))))))..)))......... ( -13.80)
>DroYak_CAF1 11052 96 - 1
CGUGCCCCACAAAA-AAAAAAAAAAGACGCGCAAAAUUUAUGCACAUUUUGAUGACAUUUUGAACGCAUAACGCAAAAUGUCAAAUACAUAAAAAUG
.((((.........-.............))))....((((((((.....)).((((((((((..((.....))))))))))))....)))))).... ( -14.45)
>consensus
CACAC___ACACACGUACCGAGAAAGACACGCGAAAUUUAUGCACAUUUUGAUGACAUUUUGAACGCAUAACGCAAAAUGUCAAAUACAUAAAAAUG
...............................((((((........)))))).((((((((((..((.....)))))))))))).............. (-12.07 = -11.70 +  -0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:25 2006