Locus 6824

Sequence ID X_DroMel_CAF1
Location 16,979,150 – 16,979,324
Length 174
Max. P 0.996995
window11170 window11171 window11172

overview

Window 0

Location 16,979,150 – 16,979,259
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.89
Mean single sequence MFE -20.38
Consensus MFE -16.95
Energy contribution -15.98
Covariance contribution -0.97
Combinations/Pair 1.35
Mean z-score -1.59
Structure conservation index 0.83
SVM decision value 0.10
SVM RNA-class probability 0.585070
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16979150 109 - 22224390
----UCCCUACAGCGUUGUGGUAUUC-AAUUGGACCACAAUAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGCCUCAAAAAUGCAACCUUAAUAAAGC-AAUAAAUCAAC-----
----..........((((((((....-......))))))))........(((((.(((((((((....)))).)))))........(((............))-)...)))))..----- ( -20.30)
>DroSec_CAF1 7282 114 - 1
----UCUCUACAGCGUUGUGGUAUUC-AAUUGGACCACAGGAAACCCCAUGGUUAGCUAUUCCUCUUAAGGGCAUGGCCUCAAAAAUGCAACCUUAAUAAAGC-AAUAAAUCAACAAAAC
----..........(((((..((((.-..((((((((..((....))..))))).(((((((((....)))).)))))..........)))....))))..))-)))............. ( -20.60)
>DroSim_CAF1 6081 114 - 1
----UCUCUACAGCGUUGUGGUAUUC-AACUGGACCACAAUAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUAGCCUCAAAAAUGAAACCUUAAUAAAGC-AAUAAAUCAACAAAAC
----........((((((((((....-......))))))))........(((...(((((((((....)))).))))).)))...................))-................ ( -20.00)
>DroEre_CAF1 7373 114 - 1
----UCUCUACAGCGUUGUGGUAUUC-AAUUGGACUACAACAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGGCUCAAAAAUGCAACCUUAAUAAAGC-AAUAAAUCAACAACAC
----........((((((((((....-......))))))))....((((((.........((((....)))))))))).......................))-................ ( -20.20)
>DroWil_CAF1 85703 116 - 1
UAAAUCAAUAAAUUGUUGUAGUAUUCUAAAUGGACUACAACAAAC----UGAUAAACUACUCCUCUUAAGGAUAUCGUCUCGAAGAUAUAACCUUAAUAAAGUUCAAAAAUCAACAAAGU
............((((((((((..((.....))))))))))))..----((((.....(((....(((((((((((........)))))..))))))...)))......))))....... ( -20.80)
>DroYak_CAF1 7923 114 - 1
----UUCCCACAGCGUUGUGGUAUUC-AACUGGACUACAACAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGGCUCAAAAGUGCAACCUUAAUAAAGC-AAUAAAUCAACAAAAC
----..........((((((((....-......))))))))........(((((...((((.((.((((((...((.(((....))).)).))))))...)).-)))))))))....... ( -20.40)
>consensus
____UCUCUACAGCGUUGUGGUAUUC_AAUUGGACCACAACAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGCCUCAAAAAUGCAACCUUAAUAAAGC_AAUAAAUCAACAAAAC
..............((((((((...........))))))))........(((((...........((((((((((..........))))..))))))...........)))))....... (-16.95 = -15.98 +  -0.97)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,979,184 – 16,979,291
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.85
Mean single sequence MFE -29.62
Consensus MFE -25.71
Energy contribution -25.22
Covariance contribution -0.49
Combinations/Pair 1.37
Mean z-score -3.18
Structure conservation index 0.87
SVM decision value 1.77
SVM RNA-class probability 0.976211
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16979184 107 - 22224390
UUAUCCGUCCAAAACUAAAACUGCAGCGUUGA------------UCCCUACAGCGUUGUGGUAUUC-AAUUGGACCACAAUAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGCCU
......((((((.......((..((((((((.------------......))))))))..))....-..))))))....................(((((((((....)))).))))).. ( -29.52)
>DroSec_CAF1 7321 103 - 1
----CCGUCCAAAACUAAAACUGCAGCGUUGA------------UCUCUACAGCGUUGUGGUAUUC-AAUUGGACCACAGGAAACCCCAUGGUUAGCUAUUCCUCUUAAGGGCAUGGCCU
----((((((((.......((..((((((((.------------......))))))))..))....-..))))))....((.....))..))...(((((((((....)))).))))).. ( -31.62)
>DroSim_CAF1 6120 107 - 1
UUAUCCGUCCAAAACUAAAACUGCAGCGUUGA------------UCUCUACAGCGUUGUGGUAUUC-AACUGGACCACAAUAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUAGCCU
......(((((........((..((((((((.------------......))))))))..))....-...)))))....................(((((((((....)))).))))).. ( -28.76)
>DroEre_CAF1 7412 107 - 1
AUAUCCGUCCAAAACUAAAACUGCAGCGUUGA------------UCUCUACAGCGUUGUGGUAUUC-AAUUGGACUACAACAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGGCU
......((((((.......((..((((((((.------------......))))))))..))....-..))))))..........((((((.........((((....)))))))))).. ( -31.12)
>DroWil_CAF1 85743 114 - 1
UU--ACGUCCAUCACUAAAACUAUAGCAAUGAGAUUUUCAUAAAUCAAUAAAUUGUUGUAGUAUUCUAAAUGGACUACAACAAAC----UGAUAAACUACUCCUCUUAAGGAUAUCGUCU
..--..((((((.......(((((((((((..(((((....))))).....))))))))))).......))))))..........----.((((......((((....)))))))).... ( -24.24)
>DroYak_CAF1 7962 107 - 1
UUAUCCGUCCAAAACUAAAACUGCAGCGCUGA------------UUCCCACAGCGUUGUGGUAUUC-AACUGGACUACAACAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGGCU
......(((((........((..((((((((.------------......))))))))..))....-...)))))..........((((((.........((((....)))))))))).. ( -32.46)
>consensus
UUAUCCGUCCAAAACUAAAACUGCAGCGUUGA____________UCUCUACAGCGUUGUGGUAUUC_AAUUGGACCACAACAAACCCCAUGAUUAGCUAUUCCUCUUAAGGGCAUGGCCU
......((((((.......((((((((((((...................)))))))))))).......))))))....................(((((((((....)))).))))).. (-25.71 = -25.22 +  -0.49)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,979,224 – 16,979,324
Length 100
Sequences 4
Columns 100
Reading direction reverse
Mean pairwise identity 91.83
Mean single sequence MFE -25.70
Consensus MFE -23.76
Energy contribution -24.57
Covariance contribution 0.81
Combinations/Pair 1.15
Mean z-score -3.24
Structure conservation index 0.92
SVM decision value 2.78
SVM RNA-class probability 0.996995
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16979224 100 - 22224390
ACUAAAGUUAAGCAUUAUUCACCAAGGGUAUCAUUAUCCGUCCAAAACUAAAACUGCAGCGUUGAUCCCUACAGCGUUGUGGUAUUCAAUUGGACCACAA
.........................(((((....)))))((((((.......((..((((((((.......))))))))..))......))))))..... ( -26.82)
>DroSim_CAF1 6160 100 - 1
ACUAUAGUUAAGCAUUAUUCACCAAGAGUAUCAUUAUCCGUCCAAAACUAAAACUGCAGCGUUGAUCUCUACAGCGUUGUGGUAUUCAACUGGACCACAA
...............(((((.....))))).........(((((........((..((((((((.......))))))))..)).......)))))..... ( -22.76)
>DroEre_CAF1 7452 100 - 1
ACUAUAGAUACACAUUACUCACCAAGAGGAUCAAUAUCCGUCCAAAACUAAAACUGCAGCGUUGAUCUCUACAGCGUUGUGGUAUUCAAUUGGACUACAA
......((((.......(((.....)))......)))).((((((.......((..((((((((.......))))))))..))......))))))..... ( -25.64)
>DroYak_CAF1 8002 100 - 1
ACUAUAGAUAAGCAUUGUUCACCAAGAGUAUCAUUAUCCGUCCAAAACUAAAACUGCAGCGCUGAUUCCCACAGCGUUGUGGUAUUCAACUGGACUACAA
......((((..(.(((.....))))..)))).......(((((........((..((((((((.......))))))))..)).......)))))..... ( -27.56)
>consensus
ACUAUAGAUAAGCAUUAUUCACCAAGAGUAUCAUUAUCCGUCCAAAACUAAAACUGCAGCGUUGAUCCCUACAGCGUUGUGGUAUUCAACUGGACCACAA
......(((((....(((((.....)))))...))))).((((((.......((..((((((((.......))))))))..))......))))))..... (-23.76 = -24.57 +   0.81)

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 12:23:48 2006