Locus 2175

Sequence ID 3R_DroMel_CAF1
Location 6,233,448 – 6,233,621
Length 173
Max. P 0.977336
window3542 window3543

overview

Window 2

Location 6,233,448 – 6,233,547
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 93.60
Mean single sequence MFE -31.12
Consensus MFE -30.31
Energy contribution -30.25
Covariance contribution -0.06
Combinations/Pair 1.10
Mean z-score -1.30
Structure conservation index 0.97
SVM decision value 0.08
SVM RNA-class probability 0.575318
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6233448 99 - 27905053
AAGCCCGCUGCUGGGUUUCUUCAUGACUGCACUUUGUUCAGCUCUAAAACCCGGCGCACUGAACCCGGCAUCAGUUUUGCCGGUUAUAGGAUCGGCUCU
.((((.((.(((((((((......(((((.((...)).))).))..))))))))))).(((...((((((.......))))))...)))....)))).. ( -34.70)
>DroSec_CAF1 6487 99 - 1
AAGCCCGCUGCUGGGUUUCUUCAUGACUGCACUUUGUUCGGCUUUAAAACCCGGCGCACUGAACCCGGCAUCAGUUAUGCCGGUUAUAGGAUCGGUUCG
.((((.((.(((((((((.....(((..((.....)))))......))))))))))).(((...(((((((.....)))))))...)))....)))).. ( -31.80)
>DroSim_CAF1 8770 99 - 1
AAGCCCGCUGCUGGGUUUCUUCAUGACUGCACUUUGUUCGGCUUUAAAACCCGGCGCACUGAACCCGGCAUCAGUUAUGCCGGUUAUAGGAUCGGUUCG
.((((.((.(((((((((.....(((..((.....)))))......))))))))))).(((...(((((((.....)))))))...)))....)))).. ( -31.80)
>DroYak_CAF1 6634 98 - 1
AAGCCCGCUUCUGGGUUUCUUCAUGACUGCACUUUGUUCGGCUUCAAAACCCGGCGCACUGAACCCGGCAUCAACUAUGCUGGUUAUAGAAUCGGUUU-
(((((.((..((((((((.....(((..((.(.......))).))))))))))).)).(((...(((((((.....)))))))...)))....)))))- ( -26.20)
>consensus
AAGCCCGCUGCUGGGUUUCUUCAUGACUGCACUUUGUUCGGCUUUAAAACCCGGCGCACUGAACCCGGCAUCAGUUAUGCCGGUUAUAGGAUCGGUUCG
.((((.((.(((((((((.....(((..((.....)))))......))))))))))).(((...(((((((.....)))))))...)))....)))).. (-30.31 = -30.25 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,233,522 – 6,233,621
Length 99
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 74.41
Mean single sequence MFE -26.82
Consensus MFE -13.91
Energy contribution -16.42
Covariance contribution 2.50
Combinations/Pair 1.13
Mean z-score -2.32
Structure conservation index 0.52
SVM decision value 1.79
SVM RNA-class probability 0.977336
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6233522 99 + 27905053
---------------CAUGAAGAAACCCAGCAGCGGGCUUCAAA-AUUUUUGGUAAUUCGGCAUAAAAAUGUCGAGCAUGCCAGCAAAACAGAA--CGCCAAUUGCCGGGAUCAGCA
---------------..........(((.((((..((((((...-....((((((.((((((((....))))))))..)))))).......)))--.)))..)))).)))....... ( -31.24)
>DroPse_CAF1 7334 86 + 1
----------------ACAAACAGA-----UAGAAAACUUCGUAAAUUCAUAUAAAUUCUGCAUAAAAAUGUCGAGCACGCCAGAAAA----------UGAAUUGCAGCGCUCAGCG
----------------.........-----...........((((.(((((.....(((.((((....)))).)))..(....)...)----------)))))))).((.....)). (  -9.00)
>DroSec_CAF1 6561 99 + 1
---------------CAUGAAGAAACCCAGCAGCGGGCUUCACA-AUUUUUGGUAAUUCGGCAUAAAAAUGUCGAGCAUGCCAGCAAAACAGAA--CGCCAAUUGCCGGGAUCAGCA
---------------..........(((.((((..((((((...-....((((((.((((((((....))))))))..)))))).......)))--.)))..)))).)))....... ( -31.24)
>DroSim_CAF1 8844 99 + 1
---------------CAUGAAGAAACCCAGCAGCGGGCUUCACA-AUUUUUGGUAAUUCGGCAUAAAAAUGUCGAGCAUGCCAGCAAAACAGAA--CGCCAAUUGCCGGGAUCAGCA
---------------..........(((.((((..((((((...-....((((((.((((((((....))))))))..)))))).......)))--.)))..)))).)))....... ( -31.24)
>DroYak_CAF1 6707 99 + 1
---------------CAUGAAGAAACCCAGAAGCGGGCUUUAGA-AUUUUUGGUAAUUCGGCAGAAAAAUGUCGAGCAUGCCAGCAAAACAGAA--AGCCAAUUGCCGGGAUCAGCG
---------------..........(((.(.....((((((...-.(((((((((.(((((((......)))))))..)))))).)))....))--)))).....).)))....... ( -27.90)
>DroAna_CAF1 9105 115 + 1
AACCAACUAAAAACAAAUGAAAUGAGUCGAAAGCUUGCUGCGAA-A-UUUUGGUAAUUCGGCAUAAAAAUGUCGAGCACGCCAGAAAGCCAGAAACUGCUAACUGCAGCGAUCAGCG
.................(((...(((.(....))))((((((..-.-(((((((..((((((((....))))))))...)))))))(((........)))...))))))..)))... ( -30.30)
>consensus
_______________CAUGAAGAAACCCAGCAGCGGGCUUCAAA_AUUUUUGGUAAUUCGGCAUAAAAAUGUCGAGCAUGCCAGCAAAACAGAA__CGCCAAUUGCCGGGAUCAGCA
.........................(((.((((..(((...........(((((..((((((((....))))))))...))))).............)))..)))).)))....... (-13.91 = -16.42 +   2.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:12 2006