Locus 1231

Sequence ID X_DroMel_CAF1
Location 3,664,893 – 3,665,036
Length 143
Max. P 0.999449
window1983 window1984 window1985

overview

Window 3

Location 3,664,893 – 3,665,008
Length 115
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 83.33
Mean single sequence MFE -29.58
Consensus MFE -26.45
Energy contribution -26.45
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.75
Structure conservation index 0.89
SVM decision value 0.86
SVM RNA-class probability 0.869746
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3664893 115 - 22224390
UAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCAACACGUCAAACGGCGAGCAGAAUGUUGCUUAUCAAUUUCUU
..((((((((((((.......))))).....((.((((((....)))))).)).............)))))))....((((....))))(((((....)))))............ ( -33.70)
>DroSec_CAF1 16712 115 - 1
UAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCAACACGCCAAUUAACGAGCAGAAUGGUGCUUAUCAAUUUCUU
..((((((((((((.......))))).....((.((((((....)))))).)).............)))))))....(((((.((........)).))))).............. ( -31.60)
>DroYak_CAF1 19181 115 - 1
AAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCCACAUAACGACCACAGAGCAGAAAAAUUCUUAUCAAUUUCUU
..((((((((((((.......))))).....((.((((((....)))))).)).............)))))))...............((..(((.....)))..))........ ( -27.00)
>DroAna_CAF1 22546 102 - 1
AAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCCUCUUGUCAGCCAC------GAAUUUUUCUUCCC-------C
..((((((((((((.......))))).....((.((((((....)))))).)).............)))))))..............------..............-------. ( -26.00)
>consensus
AAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCAACACGUCAACCACCGAGCAGAAUGUUGCUUAUCAAUUUCUU
..((((((((((((.......))))).....((.((((((....)))))).)).............))))))).......................................... (-26.45 = -26.45 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,664,933 – 3,665,036
Length 103
Sequences 3
Columns 104
Reading direction forward
Mean pairwise identity 81.29
Mean single sequence MFE -26.74
Consensus MFE -25.40
Energy contribution -25.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.52
Structure conservation index 0.95
SVM decision value 1.97
SVM RNA-class probability 0.984296
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3664933 103 + 22224390
UUGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUA-ACGAUAUGUUUUCUUUUUUGUUAAAAAA
..(((((((.(((((........)))))(((((.......)))))....(((((.......))))))))))))((-((((.............))))))..... ( -27.22)
>DroSec_CAF1 16752 87 + 1
UUGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUA-ACCAUGUGUUUU----------------
..(((((((.(((((........)))))(((((.......)))))....(((((.......))))))))))))..-............---------------- ( -25.40)
>DroYak_CAF1 19221 99 + 1
UGGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUUGAGGAGAUU-----UUUUUUGUUGAUAAA
..(((((((.(((((........)))))(((((.......)))))....(((((.......))))))))))))(..(.((((..-----..)))).)..).... ( -27.60)
>consensus
UUGGUUCCAUGGUGUAAUGGUUAGCACUCAGGACUCUGAAUCCUGCGAUCCGAGUUCAAAUCUCGGUGGAACCUA_ACGAUAUGUUUU_UUUUUUGUU_A_AAA
..(((((((.(((((........)))))(((((.......)))))....(((((.......))))))))))))............................... (-25.40 = -25.40 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,664,933 – 3,665,036
Length 103
Sequences 3
Columns 104
Reading direction reverse
Mean pairwise identity 81.29
Mean single sequence MFE -26.60
Consensus MFE -26.60
Energy contribution -26.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.02
Structure conservation index 1.00
SVM decision value 3.61
SVM RNA-class probability 0.999449
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3664933 103 - 22224390
UUUUUUAACAAAAAAGAAAACAUAUCGU-UAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCAA
............................-..((((((((((((.......))))).....((.((((((....)))))).)).............))))))).. ( -26.90)
>DroSec_CAF1 16752 87 - 1
----------------AAAACACAUGGU-UAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCAA
----------------............-..((((((((((((.......))))).....((.((((((....)))))).)).............))))))).. ( -26.90)
>DroYak_CAF1 19221 99 - 1
UUUAUCAACAAAAAA-----AAUCUCCUCAAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCCA
...............-----...........((((((((((((.......))))).....((.((((((....)))))).)).............))))))).. ( -26.00)
>consensus
UUU_U_AACAAAAAA_AAAACAUAUCGU_UAGGUUCCACCGAGAUUUGAACUCGGAUCGCAGGAUUCAGAGUCCUGAGUGCUAACCAUUACACCAUGGAACCAA
...............................((((((((((((.......))))).....((.((((((....)))))).)).............))))))).. (-26.60 = -26.60 +  -0.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:04:35 2006