Locus 8331

Sequence ID 3L_DroMel_CAF1
Location 21,821,946 – 21,822,082
Length 136
Max. P 0.923867
window13634 window13635 window13636

overview

Window 4

Location 21,821,946 – 21,822,042
Length 96
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 89.77
Mean single sequence MFE -21.31
Consensus MFE -15.81
Energy contribution -16.38
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.95
Structure conservation index 0.74
SVM decision value 1.16
SVM RNA-class probability 0.923867
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21821946 96 + 23771897
GUUCAAUAAAACCAGCAUAGAAAUCAAGCCGAAUUCAAUAUUUGGUAGCUUCCUGAUGCUAAGAAUCUACUGUCUCACGCAAGACAGUAGAUUAAA
.............(((((.........(((((((.....))))))).........)))))...((((((((((((......))))))))))))... ( -27.77)
>DroSec_CAF1 1989 87 + 1
GUUCAAUAAAACCAGCAUAGAAAUCAAGCCGAAUUCAAUAUCUGGUAGCUUCCUGAUGCUAAGAAUCUACUGUCUC---------AGUAGAUUAAA
..........(((((.((((((.((.....)).)))..))))))))(((........)))...(((((((((...)---------))))))))... ( -19.20)
>DroSim_CAF1 2049 87 + 1
UUUCAAUAAAACCAGCAUAGAAAUCAAGCCGAAUUCAAUAUCUGGUAGCUUCCUGAUGCUAAGAAUCUACUGUCUC---------AGUAGAUUAAA
..........(((((.((((((.((.....)).)))..))))))))(((........)))...(((((((((...)---------))))))))... ( -19.20)
>DroEre_CAF1 1992 95 + 1
GUUCAA-AAAACCAGCAUACAAAUCAAGCCGAAUUCAAUAUCUGGUAGCUUCCUGAUGCUUAGAAUCUACUGCAUCACGCAUGACAGUAGAUUAAA
......-......(((((.........((((.((.....)).)))).........)))))...((((((((((((.....))).)))))))))... ( -19.07)
>consensus
GUUCAAUAAAACCAGCAUAGAAAUCAAGCCGAAUUCAAUAUCUGGUAGCUUCCUGAUGCUAAGAAUCUACUGUCUC_________AGUAGAUUAAA
..........(((((.((((((.((.....)).)))..))))))))(((........)))...(((((((((............)))))))))... (-15.81 = -16.38 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,821,946 – 21,822,042
Length 96
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 89.77
Mean single sequence MFE -22.88
Consensus MFE -16.49
Energy contribution -17.93
Covariance contribution 1.44
Combinations/Pair 1.04
Mean z-score -2.01
Structure conservation index 0.72
SVM decision value 0.36
SVM RNA-class probability 0.704932
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21821946 96 - 23771897
UUUAAUCUACUGUCUUGCGUGAGACAGUAGAUUCUUAGCAUCAGGAAGCUACCAAAUAUUGAAUUCGGCUUGAUUUCUAUGCUGGUUUUAUUGAAC
...(((((((((((((....))))))))))))).(((((((.(((((....((.(((.....))).)).....))))))))))))........... ( -27.40)
>DroSec_CAF1 1989 87 - 1
UUUAAUCUACU---------GAGACAGUAGAUUCUUAGCAUCAGGAAGCUACCAGAUAUUGAAUUCGGCUUGAUUUCUAUGCUGGUUUUAUUGAAC
...((((((((---------(...))))))))).......((((......(((((.(((.(((.((.....)).))).))))))))....)))).. ( -20.30)
>DroSim_CAF1 2049 87 - 1
UUUAAUCUACU---------GAGACAGUAGAUUCUUAGCAUCAGGAAGCUACCAGAUAUUGAAUUCGGCUUGAUUUCUAUGCUGGUUUUAUUGAAA
...((((((((---------(...))))))))).......((((......(((((.(((.(((.((.....)).))).))))))))....)))).. ( -20.30)
>DroEre_CAF1 1992 95 - 1
UUUAAUCUACUGUCAUGCGUGAUGCAGUAGAUUCUAAGCAUCAGGAAGCUACCAGAUAUUGAAUUCGGCUUGAUUUGUAUGCUGGUUUU-UUGAAC
...(((((((((.(((.....)))))))))))).......(((((((...(((((....((((((......))))))....))))))))-)))).. ( -23.50)
>consensus
UUUAAUCUACU_________GAGACAGUAGAUUCUUAGCAUCAGGAAGCUACCAGAUAUUGAAUUCGGCUUGAUUUCUAUGCUGGUUUUAUUGAAC
...((((((((((..........)))))))))).......((((......(((((.(((.(((.((.....)).))).))))))))....)))).. (-16.49 = -17.93 +   1.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,821,978 – 21,822,082
Length 104
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 88.94
Mean single sequence MFE -21.70
Consensus MFE -16.46
Energy contribution -17.02
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -2.28
Structure conservation index 0.76
SVM decision value 0.96
SVM RNA-class probability 0.891122
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21821978 104 + 23771897
AUUCAAUAUUUGGUAGCUUCCUGAUGCUAAGAAUCUACUGUCUCACGCAAGACAGUAGAUUAAAUCAGAUUAUUUAUUUGCAUGUUUAAAUUAAACGGAAUUUA
((((...((((((((((........)))...((((((((((((......))))))))))))..)))))))............((((((...))))))))))... ( -24.50)
>DroSec_CAF1 2021 95 + 1
AUUCAAUAUCUGGUAGCUUCCUGAUGCUAAGAAUCUACUGUCUC---------AGUAGAUUAAAUCAGAUUAUUUAUUUGCAUGUUUAACUUAAACGGAAUUUA
((((...((((((((((........)))...(((((((((...)---------))))))))..)))))))............((((((...))))))))))... ( -19.90)
>DroSim_CAF1 2081 95 + 1
AUUCAAUAUCUGGUAGCUUCCUGAUGCUAAGAAUCUACUGUCUC---------AGUAGAUUAAAUCAGAUUAUUUAUUUGCAUGUUUAACUUAAACGGAAUUUA
((((...((((((((((........)))...(((((((((...)---------))))))))..)))))))............((((((...))))))))))... ( -19.90)
>DroEre_CAF1 2023 104 + 1
AUUCAAUAUCUGGUAGCUUCCUGAUGCUUAGAAUCUACUGCAUCACGCAUGACAGUAGAUUAAAUCAGAUUAUUAAUUUCCAUGCUUAAAUUAAUCGGAAUUUU
((((...((((((((((........)))...((((((((((((.....))).)))))))))..))))))).((((((((........))))))))..))))... ( -22.50)
>consensus
AUUCAAUAUCUGGUAGCUUCCUGAUGCUAAGAAUCUACUGUCUC_________AGUAGAUUAAAUCAGAUUAUUUAUUUGCAUGUUUAAAUUAAACGGAAUUUA
((((...((((((((((........)))...(((((((((............)))))))))..)))))))............((((((...))))))))))... (-16.46 = -17.02 +   0.56)

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 13:12:48 2006