Locus 2588

Sequence ID 2L_DroMel_CAF1
Location 7,169,241 – 7,169,368
Length 127
Max. P 0.996756
window4124 window4125 window4126

overview

Window 4

Location 7,169,241 – 7,169,344
Length 103
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.58
Mean single sequence MFE -29.82
Consensus MFE -18.91
Energy contribution -19.47
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -3.01
Structure conservation index 0.63
SVM decision value 1.42
SVM RNA-class probability 0.952304
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7169241 103 - 22407834
GGCAGUUUUUAAUUGCGCCAUAAAUCAAAUCUACG--AUAAAUGG-CAAGCAGUUAAAGGGCUGCUAACCAAAUGGGAGCCAUAAGCUGAUAACAGACU--------------GUGUAUA
.((((((((((((((((((((..(((........)--))..))))-)..))))))))).((((.(((......))).))))..............))))--------------))..... ( -31.30)
>DroSec_CAF1 110517 103 - 1
GGCAGUUUUUAAUUGCGCCAUAAAUCAAAUCUACG--AUAAAUGG-CAAGCAGUUAAAGGGCUGCUAACCAAAUGGGAGCCAUAAGCUGAUAACAGACU--------------GUGUAUA
.((((((((((((((((((((..(((........)--))..))))-)..))))))))).((((.(((......))).))))..............))))--------------))..... ( -31.30)
>DroWil_CAF1 185272 116 - 1
---GAUUUUUAAUUGCGCCAUAAAUCAAAUCUAGGAGAUAAAUGGGCCAACAGUUAAAGGGCUGCUAACCAAAUGGGAGCCAUAAGCUGAUAAGAGAGAGAGAGCAACUGACUUUUCA-G
---..((((((...((.((((..(((..........)))..))))))...(((((....((((.(((......))).))))...))))).)))))).(((((..(....)..))))).-. ( -24.00)
>DroAna_CAF1 116593 101 - 1
GGCAGUUUUUAAUUGCGCCAUAAAUCAAAUCUACG--AUAAAUGG-CA-GCAGUUAAAGGGCUGCUAACCAAAUGGGAGCCAUAAGCUGAUAACAGACU--------------GUGUA-A
.((((((((((((((((((((..(((........)--))..))))-).-))))))))).((((.(((......))).))))..............))))--------------))...-. ( -32.70)
>consensus
GGCAGUUUUUAAUUGCGCCAUAAAUCAAAUCUACG__AUAAAUGG_CAAGCAGUUAAAGGGCUGCUAACCAAAUGGGAGCCAUAAGCUGAUAACAGACU______________GUGUA_A
..((((((((((((((.((((....................))))....))))))))).((((.(((......))).))))...)))))............................... (-18.91 = -19.47 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,169,267 – 7,169,368
Length 101
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 86.87
Mean single sequence MFE -34.37
Consensus MFE -28.42
Energy contribution -28.53
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -2.21
Structure conservation index 0.83
SVM decision value 0.67
SVM RNA-class probability 0.818556
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7169267 101 + 22407834
GCUCCCAUUUGGUUAGCAGCCCUUUAACUGCUUGCCAUUUAUCGUAGAUUUGAUUUAUGGCGCAAUUAAAAACUGCCCCAGAUGAAAA-------------GUGGGGGGGG---GGU
((((((.((((((((((((........))))).(((((..((((......))))..)))))..))))))).....(((((..(....)-------------.))))).)))---))) ( -36.00)
>DroSec_CAF1 110543 101 + 1
GCUCCCAUUUGGUUAGCAGCCCUUUAACUGCUUGCCAUUUAUCGUAGAUUUGAUUUAUGGCGCAAUUAAAAACUGCCCCAGAUGAAAA-------------GUGGGCGGAG---GUU
.(((((((((((...((((...(((((.(((..(((((..((((......))))..)))))))).)))))..)))).)))))))....-------------(....)))))---... ( -32.50)
>DroAna_CAF1 116618 116 + 1
GCUCCCAUUUGGUUAGCAGCCCUUUAACUGC-UGCCAUUUAUCGUAGAUUUGAUUUAUGGCGCAAUUAAAAACUGCCCCAGAUGAAAAAGACGGCGAUGGUGUGGAGGGACGAUGGU
.(((((((((((...((((...(((((.(((-.(((((..((((......))))..)))))))).)))))..)))).)))))))......(((.(...).))))))).......... ( -34.60)
>consensus
GCUCCCAUUUGGUUAGCAGCCCUUUAACUGCUUGCCAUUUAUCGUAGAUUUGAUUUAUGGCGCAAUUAAAAACUGCCCCAGAUGAAAA_____________GUGGGGGGAG___GGU
.(((((((((((...((((...(((((.(((..(((((..((((......))))..)))))))).)))))..)))).)))))))...................)))).......... (-28.42 = -28.53 +   0.11)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,169,267 – 7,169,368
Length 101
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 86.87
Mean single sequence MFE -33.30
Consensus MFE -32.47
Energy contribution -32.47
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.36
Structure conservation index 0.97
SVM decision value 2.74
SVM RNA-class probability 0.996756
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 7169267 101 - 22407834
ACC---CCCCCCCCAC-------------UUUUCAUCUGGGGCAGUUUUUAAUUGCGCCAUAAAUCAAAUCUACGAUAAAUGGCAAGCAGUUAAAGGGCUGCUAACCAAAUGGGAGC
...---..........-------------((..(((.((((((((((((((((((((((((..(((........)))..)))))..))))))))).)))))))..))).)))..)). ( -32.50)
>DroSec_CAF1 110543 101 - 1
AAC---CUCCGCCCAC-------------UUUUCAUCUGGGGCAGUUUUUAAUUGCGCCAUAAAUCAAAUCUACGAUAAAUGGCAAGCAGUUAAAGGGCUGCUAACCAAAUGGGAGC
...---((((.((((.-------------........))))((((((((((((((((((((..(((........)))..)))))..))))))))).))))))..........)))). ( -33.40)
>DroAna_CAF1 116618 116 - 1
ACCAUCGUCCCUCCACACCAUCGCCGUCUUUUUCAUCUGGGGCAGUUUUUAAUUGCGCCAUAAAUCAAAUCUACGAUAAAUGGCA-GCAGUUAAAGGGCUGCUAACCAAAUGGGAGC
.............................((..(((.((((((((((((((((((((((((..(((........)))..))))).-))))))))).)))))))..))).)))..)). ( -34.00)
>consensus
ACC___CUCCCCCCAC_____________UUUUCAUCUGGGGCAGUUUUUAAUUGCGCCAUAAAUCAAAUCUACGAUAAAUGGCAAGCAGUUAAAGGGCUGCUAACCAAAUGGGAGC
.............................((..(((.((((((((((((((((((((((((..(((........)))..)))))..))))))))).)))))))..))).)))..)). (-32.47 = -32.47 +  -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 10:31:20 2006