Locus 2200

Sequence ID 3L_DroMel_CAF1
Location 6,044,784 – 6,044,904
Length 120
Max. P 0.941041
window3405 window3406

overview

Window 5

Location 6,044,784 – 6,044,904
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.17
Mean single sequence MFE -46.47
Consensus MFE -30.98
Energy contribution -30.32
Covariance contribution -0.66
Combinations/Pair 1.53
Mean z-score -2.27
Structure conservation index 0.67
SVM decision value 1.31
SVM RNA-class probability 0.941041
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6044784 120 + 23771897
GUGCCCGUGGGCAUAUACUCCGCUGCCUUGGCCAUCAUGGGUCGAUUCUUUGUAAACAUUAGCUAUAAUAUUGGUUUGCAAUGGGCGGCGGAGGUCCUGCCCACUGUGGUUAGGGCGCAG
(((((((((((((....((((((((((((((((......))))))....((((((((..((.......))...))))))))..))))))))))....)))))))((....)))))))).. ( -58.50)
>DroVir_CAF1 149302 120 + 1
GUGCCCGUGGGCGUGUACUCGGCCACAUUGGCCAUUAUGGGCCGAUUCUUUGUGAACAUCAGCUACAACAUUGGACUGCAGUAUGCGGCCGAGAUAUUGCCGACGGUGGUGCGCGCCCAG
.......(((((((((.(((((((..(((((((......))))))).....(((.((..((((((......))).)))..)).))))))))))..((..((...))..))))))))))). ( -50.40)
>DroGri_CAF1 147064 120 + 1
GUGCCCGUGGGCGUCUACUCGGCCACGUUAGCCAUUAUGGGUCGCUUCUUUGUCAACAUUAGCUACAAUAUUGGACUGCAGUAUGCGGCCGAGAUUCUGCCCACUGUGGUGCGUGCCCAG
(..((((((((((....(((((((.(((((((((.(((..((.(((....((....))..))).)).))).))).)))....))).)))))))....))))))).).))..)........ ( -46.30)
>DroWil_CAF1 223937 120 + 1
GUGCCGGUGGGUGUUUAUUCCGCUGCCUUGGCCAUUAUGGGUAGAUUCUUUGUCAAUAUUAGCUAUAACAUUGGCCUACAAUGGGCUGCCGAAGUUUUGCCCACUGUGGUGAGAGCUCAA
....(((((((((....(((.((.((((.(((((((((((.(((((.....))).....)).))))))...)))))......)))).)).)))....)))))))))((((....)).)). ( -39.70)
>DroMoj_CAF1 117389 120 + 1
GCACCGGUAGGCGUAUAUUCCGCUACGUUGGCUAUAAUGGGUCGUUUCUUUGUGAACAUUAGCUAUAAUAUUGGACUGCAGUAUGCAGCUGAGAUAUUACCCACUGUAGUGCGUGCUCAG
(((((.((((.((.......))))))....((((((.(((((.((.((..((....))((((((...((((((.....))))))..)))))))).)).))))).))))))).)))).... ( -35.80)
>DroAna_CAF1 107894 120 + 1
GUGCCCGUGGGAGUUUACUCCGCGGCCUUGGCUAUAAUGGGUCGAUUUUUCGUAAACAUCAGUUAUAACAUUGGACUCCAGUGGGCUGCGGAGGUGCUGCCCACCGUGGUCAGAGCCCAG
..((((((((((((...((((((((((.(((((...(((..((((....))).)..))).)))))...((((((...))))))))))))))))..))).)))).)).))).......... ( -48.10)
>consensus
GUGCCCGUGGGCGUAUACUCCGCUACCUUGGCCAUUAUGGGUCGAUUCUUUGUAAACAUUAGCUAUAACAUUGGACUGCAGUAGGCGGCCGAGAUACUGCCCACUGUGGUGAGAGCCCAG
..(((.(((((((....(((((((.((((((((......)))))).......................(((((.....))))))).)))))))....)))))))...))).......... (-30.98 = -30.32 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,044,784 – 6,044,904
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.17
Mean single sequence MFE -38.72
Consensus MFE -21.94
Energy contribution -21.58
Covariance contribution -0.36
Combinations/Pair 1.42
Mean z-score -1.94
Structure conservation index 0.57
SVM decision value 0.44
SVM RNA-class probability 0.736229
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6044784 120 - 23771897
CUGCGCCCUAACCACAGUGGGCAGGACCUCCGCCGCCCAUUGCAAACCAAUAUUAUAGCUAAUGUUUACAAAGAAUCGACCCAUGAUGGCCAAGGCAGCGGAGUAUAUGCCCACGGGCAC
....((((........(((((((....((((((.(((....((.....(((((((....)))))))........((((.....)))).))...))).))))))....))))))))))).. ( -40.30)
>DroVir_CAF1 149302 120 - 1
CUGGGCGCGCACCACCGUCGGCAAUAUCUCGGCCGCAUACUGCAGUCCAAUGUUGUAGCUGAUGUUCACAAAGAAUCGGCCCAUAAUGGCCAAUGUGGCCGAGUACACGCCCACGGGCAC
.(((.......)))((((.(((.....(((((((((((.((((((.......))))))...................((((......)))).))))))))))).....))).)))).... ( -46.50)
>DroGri_CAF1 147064 120 - 1
CUGGGCACGCACCACAGUGGGCAGAAUCUCGGCCGCAUACUGCAGUCCAAUAUUGUAGCUAAUGUUGACAAAGAAGCGACCCAUAAUGGCUAACGUGGCCGAGUAGACGCCCACGGGCAC
........((.((...((((((.....(((((((((........(((.(((((((....)))))))))).....(((.(.......).)))...))))))))).....)))))))))).. ( -42.70)
>DroWil_CAF1 223937 120 - 1
UUGAGCUCUCACCACAGUGGGCAAAACUUCGGCAGCCCAUUGUAGGCCAAUGUUAUAGCUAAUAUUGACAAAGAAUCUACCCAUAAUGGCCAAGGCAGCGGAAUAAACACCCACCGGCAC
....((.....(((((((((((....(....)..))))))))).(((((.(((((..........)))))..(........)....)))))..))...(((............))))).. ( -29.70)
>DroMoj_CAF1 117389 120 - 1
CUGAGCACGCACUACAGUGGGUAAUAUCUCAGCUGCAUACUGCAGUCCAAUAUUAUAGCUAAUGUUCACAAAGAAACGACCCAUUAUAGCCAACGUAGCGGAAUAUACGCCUACCGGUGC
....((((...(((.(((((((....(((..(((((.....)))))..(((((((....))))))).....)))....))))))).))).....((((((.......)).))))..)))) ( -30.30)
>DroAna_CAF1 107894 120 - 1
CUGGGCUCUGACCACGGUGGGCAGCACCUCCGCAGCCCACUGGAGUCCAAUGUUAUAACUGAUGUUUACGAAAAAUCGACCCAUUAUAGCCAAGGCCGCGGAGUAAACUCCCACGGGCAC
...((((..(((..((((((((.((......)).))))))))..)))............(((((..(.(((....))))..))))).))))..(.(((.((((....))))..))).).. ( -42.80)
>consensus
CUGGGCACGCACCACAGUGGGCAAAACCUCGGCCGCACACUGCAGUCCAAUAUUAUAGCUAAUGUUCACAAAGAAUCGACCCAUAAUGGCCAAGGCAGCGGAGUAAACGCCCACGGGCAC
...........((...((((((.....((((((.(((...........(((((((....)))))))..............((.....))....))).)))))).....)))))).))... (-21.94 = -21.58 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:26:37 2006