Locus 6207

Sequence ID 2R_DroMel_CAF1
Location 19,539,349 – 19,539,538
Length 189
Max. P 0.972918
window9938 window9939 window9940

overview

Window 8

Location 19,539,349 – 19,539,458
Length 109
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 97.43
Mean single sequence MFE -23.08
Consensus MFE -19.89
Energy contribution -21.75
Covariance contribution 1.86
Combinations/Pair 1.03
Mean z-score -1.59
Structure conservation index 0.86
SVM decision value 0.32
SVM RNA-class probability 0.685652
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19539349 109 + 20766785
GCAAGUAUGAAAAUACAUUUGACAAUAUAGCGAAAUAUUAUGUUUUAUUAAGUUCUAUUGCGAUACAAUGGGGCUCUUUUUAUCUAUGUCAGAUAUAUUCGCGUUGUUC
((..((((....))))((((((((...(((..((((.....))))..)))((((((((((.....))))))))))...........))))))))......))....... ( -24.70)
>DroSec_CAF1 4824 109 + 1
GCAAGUAUGAAAAUACAUUUGACAAUAUAGCGAAAUAUUAUGUUUUAUUAAGUUCUAUUGCGAUACAAUGGGGCUCUUUUUAUCUAUGUCAGAUAUAUUCGCGUUGUUC
((..((((....))))((((((((...(((..((((.....))))..)))((((((((((.....))))))))))...........))))))))......))....... ( -24.70)
>DroEre_CAF1 4989 109 + 1
GCAAGUAUGAAAAUACAUUUGACAAUAUAGCGAAAUAUUAUGUUUUAUUAAGUUCUAUUGCGAUACAAUGGGGCUCUUUUUAUCUAUGUCAGAUAUAUUCGCGUUGUUC
((..((((....))))((((((((...(((..((((.....))))..)))((((((((((.....))))))))))...........))))))))......))....... ( -24.70)
>DroYak_CAF1 4831 109 + 1
GCAAGUAUGAAAAUACAUUUGACAAUAUAGCGAAAUAUUAUGUUUUAUUAAGUUCUAUUGCGAUACAAUGGGGCUCUUUUUAUCUAUGUCAGAUAUAUUCGCGUUAUUC
((..((((....))))((((((((...(((..((((.....))))..)))((((((((((.....))))))))))...........))))))))......))....... ( -24.70)
>DroAna_CAF1 4407 109 + 1
GCAAGUAUGAAAAUACAUUUGACAAUAUAGCGAAAUAUUAUGUUUUAUUAAUUUCUAUUGCGAUACAAUGGGGCUCUUUUUGUCUAUAUCAGAUAUAUUCGCGUUGUUC
....((((....))))....((((((...((((((((((...............((((((.....))))))(((.......))).......))))).))))))))))). ( -20.10)
>DroPer_CAF1 6938 106 + 1
GCAAGUAUGAAAAUACAUUUGACAAUAUAGCGAAAU---AUGUUUUAUUAACUUCUAUUGCGAUACAAUGGGGCUCUUUUUAUCUAUAUCAGAUAUAUUCGCGUUGUUC
....((((....))))....((((((...(((((..---.............((((((((.....)))))))).......(((((.....)))))..))))))))))). ( -19.60)
>consensus
GCAAGUAUGAAAAUACAUUUGACAAUAUAGCGAAAUAUUAUGUUUUAUUAAGUUCUAUUGCGAUACAAUGGGGCUCUUUUUAUCUAUGUCAGAUAUAUUCGCGUUGUUC
....((((....))))....((((((...(((((................((((((((((.....)))))))))).....(((((.....)))))..))))))))))). (-19.89 = -21.75 +   1.86)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,539,378 – 19,539,498
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.17
Mean single sequence MFE -35.82
Consensus MFE -31.64
Energy contribution -32.00
Covariance contribution 0.36
Combinations/Pair 1.17
Mean z-score -1.45
Structure conservation index 0.88
SVM decision value 0.53
SVM RNA-class probability 0.770069
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19539378 120 + 20766785
GCGAAAUAUUAUGUUUUAUUAAGUUCUAUUGCGAUACAAUGGGGCUCUUUUUAUCUAUGUCAGAUAUAUUCGCGUUGUUCUGCGGGGCAGCUCCGUUCCCAGGGCUGGCCGGGAUGGCUC
(((((................((((((((((.....)))))))))).....(((((.....)))))..)))))((..((((...((.((((.((.......)))))).))))))..)).. ( -37.70)
>DroSec_CAF1 4853 120 + 1
GCGAAAUAUUAUGUUUUAUUAAGUUCUAUUGCGAUACAAUGGGGCUCUUUUUAUCUAUGUCAGAUAUAUUCGCGUUGUUCUGCGGGGCAGCUCCGUUCCCAGGGCUGGCCGGGAUGGCUC
(((((................((((((((((.....)))))))))).....(((((.....)))))..)))))((..((((...((.((((.((.......)))))).))))))..)).. ( -37.70)
>DroEre_CAF1 5018 120 + 1
GCGAAAUAUUAUGUUUUAUUAAGUUCUAUUGCGAUACAAUGGGGCUCUUUUUAUCUAUGUCAGAUAUAUUCGCGUUGUUCUGCGGGGCAGCUCCGUUCCCAGGGCUGGCCGGGAUGGCUC
(((((................((((((((((.....)))))))))).....(((((.....)))))..)))))((..((((...((.((((.((.......)))))).))))))..)).. ( -37.70)
>DroYak_CAF1 4860 120 + 1
GCGAAAUAUUAUGUUUUAUUAAGUUCUAUUGCGAUACAAUGGGGCUCUUUUUAUCUAUGUCAGAUAUAUUCGCGUUAUUCUGCGGGGCAGCUCCGUUCCCAGGGCUGGCCGGGAUGGCUC
(((((................((((((((((.....)))))))))).....(((((.....)))))..)))))((((((((...((.((((.((.......)))))).)))))))))).. ( -37.80)
>DroAna_CAF1 4436 120 + 1
GCGAAAUAUUAUGUUUUAUUAAUUUCUAUUGCGAUACAAUGGGGCUCUUUUUGUCUAUAUCAGAUAUAUUCGCGUUGUUCUGCGGCGCAGCUCCGUUCCCAGGGCUGGCAGGAAUAGCUC
((((((((((...............((((((.....))))))(((.......))).......))))).)))))((((((((...((.((((.((.......)))))))).)))))))).. ( -34.80)
>DroPer_CAF1 6967 117 + 1
GCGAAAU---AUGUUUUAUUAACUUCUAUUGCGAUACAAUGGGGCUCUUUUUAUCUAUAUCAGAUAUAUUCGCGUUGUUCUGCGGCGCAGCACCGUUGCCGGGACUGGCUGGAAUAUUUC
(((((..---.............((((((((.....)))))))).......(((((.....)))))..)))))..(((((..((((.(((..(((....)))..)))))))))))).... ( -29.20)
>consensus
GCGAAAUAUUAUGUUUUAUUAAGUUCUAUUGCGAUACAAUGGGGCUCUUUUUAUCUAUGUCAGAUAUAUUCGCGUUGUUCUGCGGGGCAGCUCCGUUCCCAGGGCUGGCCGGGAUGGCUC
(((((................((((((((((.....)))))))))).....(((((.....)))))..)))))((((((((...((.((((((........)))))).)))))))))).. (-31.64 = -32.00 +   0.36)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,539,418 – 19,539,538
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 93.50
Mean single sequence MFE -42.65
Consensus MFE -39.34
Energy contribution -39.28
Covariance contribution -0.05
Combinations/Pair 1.12
Mean z-score -1.64
Structure conservation index 0.92
SVM decision value 1.70
SVM RNA-class probability 0.972918
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19539418 120 - 20766785
CCCAUAUCCGGCUCGAAUCCGUGGAGCAUCGACCGGGCGGGAGCCAUCCCGGCCAGCCCUGGGAACGGAGCUGCCCCGCAGAACAACGCGAAUAUAUCUGACAUAGAUAAAAAGAGCCCC
.........(((((...((.((((.((.......((.(((((....))))).))(((.(((....))).))))).)))).))............((((((...))))))....))))).. ( -43.70)
>DroSec_CAF1 4893 120 - 1
CCCAUCUCCGGCUCGAAUCCGUGGAGCAUCGACCGGGCGGGAGCCAUCCCGGCCAGCCCUGGGAACGGAGCUGCCCCGCAGAACAACGCGAAUAUAUCUGACAUAGAUAAAAAGAGCCCC
.........(((((...((.((((.((.......((.(((((....))))).))(((.(((....))).))))).)))).))............((((((...))))))....))))).. ( -43.70)
>DroEre_CAF1 5058 120 - 1
CCCAUCUCCGGCUCAAAUCCGUGGAGCAUCGACCGGGCGGGAGCCAUCCCGGCCAGCCCUGGGAACGGAGCUGCCCCGCAGAACAACGCGAAUAUAUCUGACAUAGAUAAAAAGAGCCCC
.........(((((...((.((((.((.......((.(((((....))))).))(((.(((....))).))))).)))).))............((((((...))))))....))))).. ( -43.70)
>DroYak_CAF1 4900 120 - 1
CCCAUCUCCGGCUCGAAUCCGUGGAGCAUCGACCGGGCGGGAGCCAUCCCGGCCAGCCCUGGGAACGGAGCUGCCCCGCAGAAUAACGCGAAUAUAUCUGACAUAGAUAAAAAGAGCCCC
.........(((((...((.((((.((.......((.(((((....))))).))(((.(((....))).))))).)))).))............((((((...))))))....))))).. ( -43.70)
>DroAna_CAF1 4476 120 - 1
CCCAUCUCCGGCUCGAAUCCGUGGAGUAUUGACCGGGCGGGAGCUAUUCCUGCCAGCCCUGGGAACGGAGCUGCGCCGCAGAACAACGCGAAUAUAUCUGAUAUAGACAAAAAGAGCCCC
.........(((((.....((((..((.(((..((((((((((...))))))))(((.(((....))).))).))...))).))..))))......((((...))))......))))).. ( -38.00)
>DroPer_CAF1 7004 120 - 1
CCCAUCUCUGGCUCGAAUCCGUGGAGUAUUGACCGAGCGGGAAAUAUUCCAGCCAGUCCCGGCAACGGUGCUGCGCCGCAGAACAACGCGAAUAUAUCUGAUAUAGAUAAAAAGAGCCCC
.........(((((.......(((((((((..((....))..)))))))))(((((..(((....)))..))).))(((........)))....((((((...))))))....))))).. ( -43.10)
>consensus
CCCAUCUCCGGCUCGAAUCCGUGGAGCAUCGACCGGGCGGGAGCCAUCCCGGCCAGCCCUGGGAACGGAGCUGCCCCGCAGAACAACGCGAAUAUAUCUGACAUAGAUAAAAAGAGCCCC
.........(((((...((.((((.((.......((.(((((....))))).))(((.(((....))).))))).)))).))............((((((...))))))....))))).. (-39.34 = -39.28 +  -0.05)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:31 2006