Locus 698

Sequence ID 3L_DroMel_CAF1
Location 2,090,042 – 2,090,233
Length 191
Max. P 0.954318
window1065 window1066 window1067

overview

Window 5

Location 2,090,042 – 2,090,162
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.44
Mean single sequence MFE -45.70
Consensus MFE -38.11
Energy contribution -37.67
Covariance contribution -0.44
Combinations/Pair 1.23
Mean z-score -1.77
Structure conservation index 0.83
SVM decision value 0.12
SVM RNA-class probability 0.594488
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2090042 120 - 23771897
UUCAAGAACGCUCGCUUCGCCCAGGGCGGCAAUGCCCUGUUCGAGGGACGCCUGCGUGGCAACCCGAAGCCAUUCGUGACCUGGACCCGAAAAGGCGCACCCCUUCUCGAGUCGCAGAAG
.(((.(((.(...((((((..(((((((....)))))))..)..(((..(((.....)))..))))))))).))).))).((((((.(((.((((......)))).))).))).)))... ( -46.80)
>DroVir_CAF1 167747 120 - 1
UUCAAGAACGCUCGCUUCGCUCAGGGCGGCAACGCCCUGUUUGAAGGUAGGCUGCGUGGCAACCCGAAGCCAUUCGUUACAUGGACCCGAAAAGGCGCACCACUUCUCGAGUCGCAAAAG
......((((....(((((..(((((((....)))))))..)))))...((((.((.(....).)).))))...))))...(((((.(((.(((........))).))).))).)).... ( -45.60)
>DroGri_CAF1 142385 120 - 1
UUUAAGAACGCUCGCUUCGCUCAGGGUGGCAACGCCCUGUUCGAAGGUCGGCUGCGUGGCAACCCAAAGCCAUUCGUUACAUGGACCCGAAAAGGCGCACCACUUCUCGAGUCGCAAAAG
........(((((((((((..(((((((....)))))))..)))))...((.((((((((........))).((((...........))))...)))))))......)))).))...... ( -43.80)
>DroWil_CAF1 186547 120 - 1
UUUAAAAACGCUCGCUUCGCUCAAGGCGGCAACGCCCUCUUUGAGGGUAGACUGCGUGGCAAUCCAAAGCCAUUUGUUACUUGGACCCGAAAAGGCGCACCACUUCUCGAGUCGCAAAAG
.......((((...((.(.(((((((((....))))....))))).).))...))))(((........))).........((((((.(((.(((........))).))).))).)))... ( -37.20)
>DroMoj_CAF1 146188 120 - 1
UUUAAGAACGCUCGCUUCGCUCAGGGUGGCAACGCCCUGUUCGAAGGCAGGCUCCGUGGCAACCCGAAGCCAUUCGUUACAUGGACCCGAAAAGGCGCACCACUUCUCGAGUCGCAAAAG
......((((...((((((..(((((((....)))))))..)))).)).((((.((.(....).)).))))...))))...(((((.(((.(((........))).))).))).)).... ( -45.30)
>DroAna_CAF1 149056 120 - 1
UUCAAGAACGCUCGCUUCGCCCAGGGCGGCAACGCCCUGUUCGAGGGCCGGUUGAGGGGCAACCCGAAGCCAUUCGUGACAUGGACGCGGAAAGGCGCACCCCUUCUCGAGUCGCAGAAG
........(((((((((((..(((((((....)))))))..)))))(((((((..(((....)))..)))).((((((.......))))))..)))...........)))).))...... ( -55.50)
>consensus
UUCAAGAACGCUCGCUUCGCUCAGGGCGGCAACGCCCUGUUCGAAGGUAGGCUGCGUGGCAACCCGAAGCCAUUCGUUACAUGGACCCGAAAAGGCGCACCACUUCUCGAGUCGCAAAAG
.........((...(((((..(((((((....)))))))..)))))...((((...(((....))).))))............(((.(((.(((........))).))).)))))..... (-38.11 = -37.67 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,090,082 – 2,090,202
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 86.89
Mean single sequence MFE -50.92
Consensus MFE -41.21
Energy contribution -40.63
Covariance contribution -0.58
Combinations/Pair 1.25
Mean z-score -3.40
Structure conservation index 0.81
SVM decision value 1.44
SVM RNA-class probability 0.954318
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2090082 120 - 23771897
CGCCCAGGGCGACAUCUCGCCGCCCGUCUUCGAGCAGAUCUUCAAGAACGCUCGCUUCGCCCAGGGCGGCAAUGCCCUGUUCGAGGGACGCCUGCGUGGCAACCCGAAGCCAUUCGUGAC
((..((((((((....))(((((((.....(((((.(.((.....)).)))))).........)))))))...))))))..)).(((..(((.....)))..)))(((....)))..... ( -49.24)
>DroVir_CAF1 167787 120 - 1
UGCGCAAGGUGACAUCUCACCGCCUGUAUUUGAGCAAAUCUUCAAGAACGCUCGCUUCGCUCAGGGCGGCAACGCCCUGUUUGAAGGUAGGCUGCGUGGCAACCCGAAGCCAUUCGUUAC
.(((((.(((((....)))))(((((.....((((...((.....))..)))).(((((..(((((((....)))))))..))))).))))))))))(((........)))......... ( -52.90)
>DroGri_CAF1 142425 120 - 1
UGCCCAAGGUGACAUUUCACCGCCUGUAUUCGAGCAGAUCUUUAAGAACGCUCGCUUCGCUCAGGGUGGCAACGCCCUGUUCGAAGGUCGGCUGCGUGGCAACCCAAAGCCAUUCGUUAC
.((....(((((....)))))(((......(((((.(.((.....)).))))))(((((..(((((((....)))))))..)))))...))).))(((((........)))))....... ( -48.70)
>DroWil_CAF1 186587 120 - 1
UGCUCAAGGUGAUAUUUCGCCACCCGUUUUCGAGCAAAUCUUUAAAAACGCUCGCUUCGCUCAAGGCGGCAACGCCCUCUUUGAGGGUAGACUGCGUGGCAAUCCAAAGCCAUUUGUUAC
(((((..(((((....)))))....(....))))))...........((((...((.(.(((((((((....))))....))))).).))...))))(((........)))......... ( -39.70)
>DroMoj_CAF1 146228 120 - 1
UGCCCAAGGUGACAUCUCACCGCCUGUAUUCGAGCAAAUCUUUAAGAACGCUCGCUUCGCUCAGGGUGGCAACGCCCUGUUCGAAGGCAGGCUCCGUGGCAACCCGAAGCCAUUCGUUAC
(((((..(((((....)))))((((((...(((((...((.....))..)))))(((((..(((((((....)))))))..)))))))))))...).))))...((((....)))).... ( -54.80)
>DroAna_CAF1 149096 120 - 1
CGCCCAGGGCGACAUCUCGCCACCCGUUUUUGAGCAAAUCUUCAAGAACGCUCGCUUCGCCCAGGGCGGCAACGCCCUGUUCGAGGGCCGGUUGAGGGGCAACCCGAAGCCAUUCGUGAC
.((((..(((((....)))))...((((((((((......))))))))))......(((..(((((((....)))))))..))))))).((((..(((....)))..))))......... ( -60.20)
>consensus
UGCCCAAGGUGACAUCUCACCGCCCGUAUUCGAGCAAAUCUUCAAGAACGCUCGCUUCGCUCAGGGCGGCAACGCCCUGUUCGAAGGUAGGCUGCGUGGCAACCCGAAGCCAUUCGUUAC
.......(((((....)))))(((......(((((...((.....))..)))))(((((..(((((((....)))))))..)))))...)))...(((((........)))))....... (-41.21 = -40.63 +  -0.58)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,090,122 – 2,090,233
Length 111
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 83.25
Mean single sequence MFE -38.76
Consensus MFE -27.81
Energy contribution -27.39
Covariance contribution -0.41
Combinations/Pair 1.23
Mean z-score -1.63
Structure conservation index 0.72
SVM decision value 0.03
SVM RNA-class probability 0.547847
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2090122 111 - 23771897
---------CCUACGUGCCCCCUUCGCUGACACACGUGUACGCCCAGGGCGACAUCUCGCCGCCCGUCUUCGAGCAGAUCUUCAAGAACGCUCGCUUCGCCCAGGGCGGCAAUGCCCUGU
---------..((((((...............))))))......((((((((....))(((((((.....(((((.(.((.....)).)))))).........)))))))...)))))). ( -39.10)
>DroVir_CAF1 167827 111 - 1
---------CCUAUGUACCGCCCUCGUUGACACACGUUUAUGCGCAAGGUGACAUCUCACCGCCUGUAUUUGAGCAAAUCUUCAAGAACGCUCGCUUCGCUCAGGGCGGCAACGCCCUGU
---------..........((....((.(((....)))...))((..(((((....)))))..........((((...((.....))..))))))...)).(((((((....))))))). ( -33.10)
>DroPse_CAF1 179532 120 - 1
GUGGCAUCAACUACGUGCCCCCCGCAUUGACACACGUCUAUGCCCAGGGCGACAUCUCGCCGCCGGUGUUCGAGCAGAUCUUCAAGAACGCUCGCUUCGCUCAGGGCGGCAAUGCCCUGU
..(((((.......)))))....((((.(((....))).)))).((((((((....))((((((((((..(((((.(.((.....)).))))))...))))...))))))...)))))). ( -48.30)
>DroGri_CAF1 142465 111 - 1
---------CCUAUGUACCACCGUCGUUGACACACGUCUAUGCCCAAGGUGACAUUUCACCGCCUGUAUUCGAGCAGAUCUUUAAGAACGCUCGCUUCGCUCAGGGUGGCAACGCCCUGU
---------.....((((....(.(((.(((....))).))))....(((((....)))))....)))).(((((.(.((.....)).)))))).......(((((((....))))))). ( -31.80)
>DroWil_CAF1 186627 114 - 1
------CCACCUAUGUGCCGCCUUCGUUGACACACGUGUAUGCUCAAGGUGAUAUUUCGCCACCCGUUUUCGAGCAAAUCUUUAAAAACGCUCGCUUCGCUCAAGGCGGCAACGCCCUCU
------.........(((((((((.((......))(((...((....(((((....)))))..........((((..............))))))..)))..)))))))))......... ( -31.94)
>DroPer_CAF1 157328 120 - 1
GUGGCAUCAACUACGUGCCCCCCGCAUUGACACACGUCUAUGCCCAGGGCGACAUCUCGCCGCCGGUGUUCGAGCAGAUCUUCAAGAACGCUCGCUUCGCUCAGGGCGGCAAUGCCCUGU
..(((((.......)))))....((((.(((....))).)))).((((((((....))((((((((((..(((((.(.((.....)).))))))...))))...))))))...)))))). ( -48.30)
>consensus
_________CCUACGUGCCCCCCUCGUUGACACACGUCUAUGCCCAAGGCGACAUCUCGCCGCCCGUAUUCGAGCAGAUCUUCAAGAACGCUCGCUUCGCUCAGGGCGGCAACGCCCUGU
............(((((...............)))))....((....(((((....))))).........(((((...((.....))..)))))....)).(((((((....))))))). (-27.81 = -27.39 +  -0.41)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:49 2006