Locus 5328

Sequence ID 3R_DroMel_CAF1
Location 13,959,685 – 13,959,776
Length 91
Max. P 0.997648
window8685 window8686

overview

Window 5

Location 13,959,685 – 13,959,776
Length 91
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 76.25
Mean single sequence MFE -15.22
Consensus MFE -10.60
Energy contribution -10.84
Covariance contribution 0.24
Combinations/Pair 1.25
Mean z-score -2.62
Structure conservation index 0.70
SVM decision value 2.90
SVM RNA-class probability 0.997648
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13959685 91 + 27905053
UCCCA-AUUCGA--------AACUUAUUCCAA-AAACUAUGUAUUUUCCAUAGCCAUACGAACUUUUGUAUGGCUAUGAAUCACACAGUAUACAUAUAAAA-------
.....-......--------............-..(((.(((...(((.((((((((((((....)))))))))))))))..))).)))............------- ( -21.30)
>DroSec_CAF1 230576 93 + 1
UCCUAAAUUCGA--------ACCUUAUUCCAAAAAACUAUGUAUUUUCCAUAGCUUUACGAACUUUUGUAUGGCUAUGAAUCACACAGUAUACCUAUAAAA-------
............--------...............(((.(((...(((.((((((.(((((....))))).)))))))))..))).)))............------- ( -15.20)
>DroSim_CAF1 239033 92 + 1
UCCUAAAUUCGA--------ACCUUAUUCCAA-AAACUAUGUAUUUUCCAUAGCUUUACGAACUUUUGUAUGGCUAUGAAUCACACAGUAUACCUAUAAAA-------
............--------............-..(((.(((...(((.((((((.(((((....))))).)))))))))..))).)))............------- ( -15.20)
>DroEre_CAF1 221963 90 + 1
UCCUA-AUUCGA--------ACCUUAUUCCAA--AACUAUGUAUUUUCCAUAGCUUUAUGAACUUUUGUAUGGCUAUGAAUCACACAGUAUACCUAUAAAA-------
.....-......--------............--.(((.(((...(((.((((((.((..(....)..)).)))))))))..))).)))............------- ( -12.80)
>DroAna_CAF1 224500 102 + 1
-CUCU-UUUCUGAAGUUUUCUACUAUUUCCCA-GAACC---CAUUGGCCCCAGCUAUAUAUAUUUUCAUAUGGCUUUGAAUGACACUGUAUACCCAAAAUGUAUGUUA
-....-.(((((((((........)))))..)-)))..---((((.(....((((((((........)))))))).).))))......(((((.......)))))... ( -11.60)
>consensus
UCCUA_AUUCGA________ACCUUAUUCCAA_AAACUAUGUAUUUUCCAUAGCUUUACGAACUUUUGUAUGGCUAUGAAUCACACAGUAUACCUAUAAAA_______
................................................(((((((.(((((....))))).))))))).............................. (-10.60 = -10.84 +   0.24)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,959,685 – 13,959,776
Length 91
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 76.25
Mean single sequence MFE -20.72
Consensus MFE -12.14
Energy contribution -13.54
Covariance contribution 1.40
Combinations/Pair 1.11
Mean z-score -1.95
Structure conservation index 0.59
SVM decision value 0.96
SVM RNA-class probability 0.889871
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13959685 91 - 27905053
-------UUUUAUAUGUAUACUGUGUGAUUCAUAGCCAUACAAAAGUUCGUAUGGCUAUGGAAAAUACAUAGUUU-UUGGAAUAAGUU--------UCGAAU-UGGGA
-------............((((((((.(((((((((((((........)))))))))))))...)))))))).(-((((((....))--------))))).-..... ( -29.00)
>DroSec_CAF1 230576 93 - 1
-------UUUUAUAGGUAUACUGUGUGAUUCAUAGCCAUACAAAAGUUCGUAAAGCUAUGGAAAAUACAUAGUUUUUUGGAAUAAGGU--------UCGAAUUUAGGA
-------............((((((((.((((((((..(((........)))..))))))))...))))))))..((((((......)--------)))))....... ( -19.60)
>DroSim_CAF1 239033 92 - 1
-------UUUUAUAGGUAUACUGUGUGAUUCAUAGCCAUACAAAAGUUCGUAAAGCUAUGGAAAAUACAUAGUUU-UUGGAAUAAGGU--------UCGAAUUUAGGA
-------............((((((((.((((((((..(((........)))..))))))))...)))))))).(-(((((......)--------)))))....... ( -19.60)
>DroEre_CAF1 221963 90 - 1
-------UUUUAUAGGUAUACUGUGUGAUUCAUAGCCAUACAAAAGUUCAUAAAGCUAUGGAAAAUACAUAGUU--UUGGAAUAAGGU--------UCGAAU-UAGGA
-------........((((.(((((.....)))))..))))...(((((.((((((((((.......)))))))--)))((((...))--------))))))-).... ( -19.30)
>DroAna_CAF1 224500 102 - 1
UAACAUACAUUUUGGGUAUACAGUGUCAUUCAAAGCCAUAUGAAAAUAUAUAUAGCUGGGGCCAAUG---GGUUC-UGGGAAAUAGUAGAAAACUUCAGAAA-AGAG-
.........((((((((.(((.((.((..........((((....))))......(..(((((....---)))))-..))).)).)))....)).)))))).-....- ( -16.10)
>consensus
_______UUUUAUAGGUAUACUGUGUGAUUCAUAGCCAUACAAAAGUUCGUAAAGCUAUGGAAAAUACAUAGUUU_UUGGAAUAAGGU________UCGAAU_UAGGA
...................((((((((.((((((((..(((........)))..))))))))...))))))))................................... (-12.14 = -13.54 +   1.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:04 2006