Locus 481

Sequence ID 2L_DroMel_CAF1
Location 1,405,827 – 1,406,010
Length 183
Max. P 0.964915
window769 window770 window771 window772 window773

overview

Window 9

Location 1,405,827 – 1,405,940
Length 113
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 69.37
Mean single sequence MFE -20.73
Consensus MFE -10.60
Energy contribution -12.85
Covariance contribution 2.25
Combinations/Pair 1.07
Mean z-score -2.07
Structure conservation index 0.51
SVM decision value 1.42
SVM RNA-class probability 0.952571
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1405827 113 + 22407834
CCAUAAGAACAUAAUUUAAUUAACAAUUUCUAUAUCUUUUAAUGUUGUUCCUCUC-UUAGGAGCUGAGCUCAUAAGGUUUUAAAAUACCCUUCGCUUAGAGUAUCCACUUAGCG
...((((..............((((((................))))))......-...(((.((((((......(((........)))....))))))....))).))))... ( -15.89)
>DroSec_CAF1 24063 108 + 1
CCAUAACAAUUUAAUUGAAUUAACAACUUCUAUAUCUUUUAAUGUUGUUCCACUC-CUAGGAG-----AUCAUAUUGUUAAUGAAUACCCUUUGGUUAGGGUAUUCACUUAGCG
...(((((((.....(((...((((((................))))))...(((-....)))-----.))).))))))).((((((((((......))))))))))....... ( -26.49)
>DroSim_CAF1 24264 95 + 1
CCAUAACAAUUUAAUUUAAUUAACAAUUUCUAUAUCUUU-------------CUC-CUAGGCG-----AUCAUAUUGUUAAUGAAUACCCUUUGGUUAGGGUAUUCACUUAGCG
..................(((((((((.......(((..-------------...-..)))..-----.....)))))))))(((((((((......)))))))))........ ( -19.64)
>DroYak_CAF1 24408 97 + 1
CCACUAUCC---CAUU---------AUUGCUAUAUCUUGUAAUAUUGCUUCACUCCCCAAGAG-----CUCUGAAUGUUUUGAGAUACCCUGCGUUUAGGGUAUCCACUUAGCG
.........---((.(---------(((((........)))))).)).(((((((.....)))-----...)))).(((.((.(((((((((....)))))))))))...))). ( -20.90)
>consensus
CCAUAACAAUUUAAUUUAAUUAACAAUUUCUAUAUCUUUUAAUGUUGUUCCACUC_CUAGGAG_____AUCAUAAUGUUAAUAAAUACCCUUCGGUUAGGGUAUCCACUUAGCG
............................................................................(((((((((((((((......)))))))))).))))). (-10.60 = -12.85 +   2.25)

alignment

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secondary structure

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Window 0

Location 1,405,827 – 1,405,940
Length 113
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 69.37
Mean single sequence MFE -23.17
Consensus MFE -12.45
Energy contribution -11.57
Covariance contribution -0.87
Combinations/Pair 1.44
Mean z-score -2.01
Structure conservation index 0.54
SVM decision value 1.57
SVM RNA-class probability 0.964915
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1405827 113 - 22407834
CGCUAAGUGGAUACUCUAAGCGAAGGGUAUUUUAAAACCUUAUGAGCUCAGCUCCUAA-GAGAGGAACAACAUUAAAAGAUAUAGAAAUUGUUAAUUAAAUUAUGUUCUUAUGG
........(((((((((......)))))))))......((((.((((...)))).)))-)..(((((((...((((..((((.......))))..))))....))))))).... ( -19.80)
>DroSec_CAF1 24063 108 - 1
CGCUAAGUGAAUACCCUAACCAAAGGGUAUUCAUUAACAAUAUGAU-----CUCCUAG-GAGUGGAACAACAUUAAAAGAUAUAGAAGUUGUUAAUUCAAUUAAAUUGUUAUGG
.....((((((((((((......))))))))))))((((((.((((-----(((....-)))...((((((................))))))......)))).)))))).... ( -26.79)
>DroSim_CAF1 24264 95 - 1
CGCUAAGUGAAUACCCUAACCAAAGGGUAUUCAUUAACAAUAUGAU-----CGCCUAG-GAG-------------AAAGAUAUAGAAAUUGUUAAUUAAAUUAAAUUGUUAUGG
.....((((((((((((......))))))))))))((((((.((((-----(.(....-).)-------------)..((((.......)))).......))).)))))).... ( -20.10)
>DroYak_CAF1 24408 97 - 1
CGCUAAGUGGAUACCCUAAACGCAGGGUAUCUCAAAACAUUCAGAG-----CUCUUGGGGAGUGAAGCAAUAUUACAAGAUAUAGCAAU---------AAUG---GGAUAGUGG
(((((..((((((((((......)))))))).))...((((....(-----(((.....))))...((.(((((....))))).))...---------))))---...))))). ( -26.00)
>consensus
CGCUAAGUGAAUACCCUAACCAAAGGGUAUUCAAAAACAAUAUGAG_____CUCCUAG_GAGUGGAACAACAUUAAAAGAUAUAGAAAUUGUUAAUUAAAUUAAAUUGUUAUGG
........(((((((((......))))))))).................................................................................. (-12.45 = -11.57 +  -0.87)

alignment

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secondary structure

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Window 1

Location 1,405,865 – 1,405,980
Length 115
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 76.07
Mean single sequence MFE -27.41
Consensus MFE -15.20
Energy contribution -15.88
Covariance contribution 0.68
Combinations/Pair 1.06
Mean z-score -1.88
Structure conservation index 0.55
SVM decision value 0.62
SVM RNA-class probability 0.802185
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1405865 115 + 22407834
UUAAUGUUGUUCCUCUC-UUAGGAGCUGAGCUCAUAAGGUUUUAAAAUACCCUUCGCUUAGAGUAUCCACUUAGCGAUGAAAUAAAAAGCGAAAAAAUAAACAGCCUCAUCGGCCC
....((((((((((...-..))))))...(((.....(((........)))..(((((..((((....)))))))))..........))).........))))(((.....))).. ( -23.20)
>DroSec_CAF1 24101 110 + 1
UUAAUGUUGUUCCACUC-CUAGGAG-----AUCAUAUUGUUAAUGAAUACCCUUUGGUUAGGGUAUUCACUUAGCGAUGAAAUAAAAAGCGAAAAAAUAAACAGCCUCAUCGGCCC
....((((.((((.(((-....)))-----....(((((((((((((((((((......)))))))))).))))))))).........).)))......))))(((.....))).. ( -31.00)
>DroSim_CAF1 24302 97 + 1
U-------------CUC-CUAGGCG-----AUCAUAUUGUUAAUGAAUACCCUUUGGUUAGGGUAUUCACUUAGCGAUGAAAUAAAAAGCGAAAAAAUAAACAGCCUCAUCGGCCC
.-------------...-...((((-----((..(((((((((((((((((((......)))))))))).))))))))).........((.............))...))).))). ( -27.02)
>DroEre_CAF1 24067 101 + 1
-----AUUGCUCCACUU--CAGAAG-----CUCGGCGUGUUUA-GGAUACCCUGCGU-UAGGGUAUCCACUUAGCGAUGGAAUAA-AAGCGAAAAAGCAAACAGCCUCAGCGGCCC
-----............--.....(-----((.(((.(((((.-((((((((((...-)))))))))).................-..((......))))))))))..)))..... ( -29.50)
>DroYak_CAF1 24434 111 + 1
GUAAUAUUGCUUCACUCCCCAAGAG-----CUCUGAAUGUUUUGAGAUACCCUGCGUUUAGGGUAUCCACUUAGCGAUGGAAUAAAAAGCGAAAGAGUAAACAGCCUCAUUGGCCC
......((((((......(((...(-----((..(.......((.(((((((((....))))))))))))..)))..)))......))))))...........(((.....))).. ( -26.31)
>consensus
UUAAUAUUGCUCCACUC_CUAGGAG_____CUCAUAAUGUUUAUGAAUACCCUUCGGUUAGGGUAUCCACUUAGCGAUGAAAUAAAAAGCGAAAAAAUAAACAGCCUCAUCGGCCC
.....................................((((...(((((((((......))))))))).....((.............)).........))))(((.....))).. (-15.20 = -15.88 +   0.68)

alignment

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secondary structure

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dotplot

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Window 2

Location 1,405,865 – 1,405,980
Length 115
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 76.07
Mean single sequence MFE -30.09
Consensus MFE -20.58
Energy contribution -20.74
Covariance contribution 0.16
Combinations/Pair 1.37
Mean z-score -1.92
Structure conservation index 0.68
SVM decision value 1.42
SVM RNA-class probability 0.952381
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1405865 115 - 22407834
GGGCCGAUGAGGCUGUUUAUUUUUUCGCUUUUUAUUUCAUCGCUAAGUGGAUACUCUAAGCGAAGGGUAUUUUAAAACCUUAUGAGCUCAGCUCCUAA-GAGAGGAACAACAUUAA
((((..((((((...((((.((((((((((.....(((((......)))))......)))))))))).....)))).))))))..)))).(.((((..-...)))).)........ ( -28.30)
>DroSec_CAF1 24101 110 - 1
GGGCCGAUGAGGCUGUUUAUUUUUUCGCUUUUUAUUUCAUCGCUAAGUGAAUACCCUAACCAAAGGGUAUUCAUUAACAAUAUGAU-----CUCCUAG-GAGUGGAACAACAUUAA
.((((.....))))........((((((((((....((((.....((((((((((((......))))))))))))......)))).-----.....))-))))))))......... ( -31.70)
>DroSim_CAF1 24302 97 - 1
GGGCCGAUGAGGCUGUUUAUUUUUUCGCUUUUUAUUUCAUCGCUAAGUGAAUACCCUAACCAAAGGGUAUUCAUUAACAAUAUGAU-----CGCCUAG-GAG-------------A
(((((((((((((.............))).......))))))...((((((((((((......))))))))))))...........-----.))))..-...-------------. ( -27.43)
>DroEre_CAF1 24067 101 - 1
GGGCCGCUGAGGCUGUUUGCUUUUUCGCUU-UUAUUCCAUCGCUAAGUGGAUACCCUA-ACGCAGGGUAUCC-UAAACACGCCGAG-----CUUCUG--AAGUGGAGCAAU-----
.((((.....))))..((((((...(((((-(.......((((.....(((((((((.-....)))))))))-.......).))).-----.....)--))))))))))).----- ( -32.82)
>DroYak_CAF1 24434 111 - 1
GGGCCAAUGAGGCUGUUUACUCUUUCGCUUUUUAUUCCAUCGCUAAGUGGAUACCCUAAACGCAGGGUAUCUCAAAACAUUCAGAG-----CUCUUGGGGAGUGAAGCAAUAUUAC
.((((.....))))............(((((...(((((..(((.((((((((((((......))))))))......))))...))-----)...)))))...)))))........ ( -30.20)
>consensus
GGGCCGAUGAGGCUGUUUAUUUUUUCGCUUUUUAUUUCAUCGCUAAGUGGAUACCCUAAACGAAGGGUAUUCAUAAACAAUAUGAG_____CUCCUAG_GAGUGGAACAACAUUAA
.((((.....))))........((((((((.(((..............(((((((((......)))))))))...........(((.....))).))).))))))))......... (-20.58 = -20.74 +   0.16)

alignment

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secondary structure

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Window 3

Location 1,405,904 – 1,406,010
Length 106
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 84.38
Mean single sequence MFE -28.95
Consensus MFE -23.30
Energy contribution -23.25
Covariance contribution -0.05
Combinations/Pair 1.24
Mean z-score -2.03
Structure conservation index 0.80
SVM decision value 0.48
SVM RNA-class probability 0.752469
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1405904 106 - 22407834
UUCGCUUAUCCGACUUGGAAAUCUCGCCCAGGGCCGAUGAGGCUGUUUAUUUUUUCGCUUUUUAUUUCAUCGCUAAGUGGAUACUCUAAGCGAAGGGUAUUU--UAAA
(((((((((((.((((((.......(((...)))(((((((((.............))).......))))))))))))))))).....))))))........--.... ( -25.63)
>DroSec_CAF1 24135 106 - 1
UCCGCUUAUCCGACUUGGAAAUCUCGCCCAGGGCCGAUGAGGCUGUUUAUUUUUUCGCUUUUUAUUUCAUCGCUAAGUGAAUACCCUAACCAAAGGGUAUUC--AUUA
....((((((.(.(((((.........))))).).))))))..................................((((((((((((......)))))))))--))). ( -28.10)
>DroSim_CAF1 24323 106 - 1
UCCACUUAUCCGACUUGGAAAUCUCGCCCAGGGCCGAUGAGGCUGUUUAUUUUUUCGCUUUUUAUUUCAUCGCUAAGUGAAUACCCUAACCAAAGGGUAUUC--AUUA
....((((((.(.(((((.........))))).).))))))..................................((((((((((((......)))))))))--))). ( -28.40)
>DroEre_CAF1 24095 103 - 1
UCCGCUUAUCCGACUUGGAAAUCUCGCCCAGGGCCGCUGAGGCUGUUUGCUUUUUCGCUU-UUAUUCCAUCGCUAAGUGGAUACCCUA-ACGCAGGGUAUCC---UAA
...(((((..(((..(((((.....((((((.....))).))).....((......))..-...)))))))).)))))(((((((((.-....)))))))))---... ( -33.50)
>DroYak_CAF1 24469 106 - 1
GCCGCUUAUCCGACUUGGAAAUCUCGCCCAGGGCCAAUGAGGCUGUUUACUCUUUCGCUUUUUAUUCCAUCGCUAAGUGGAUACCCUAAACGCAGGGUAUCU--CAAA
..((((((..(((..(((((.....(((...)))....(((........)))............)))))))).))))))((((((((......)))))))).--.... ( -29.20)
>DroAna_CAF1 24135 100 - 1
U-UGCUUAUCCGUUUCGGAAAUCUUGCCCAGGGCCGAUGAGGCUGUAUA-------GCUUUUGGUUUCAUCGCUUAAUGGAUACCCUAAACAAAGGGUAUAUUCGAUA
.-............(((((........(((.(((.((((((((((....-------.....)))))))))))))...)))(((((((......))))))).))))).. ( -28.90)
>consensus
UCCGCUUAUCCGACUUGGAAAUCUCGCCCAGGGCCGAUGAGGCUGUUUAUUUUUUCGCUUUUUAUUUCAUCGCUAAGUGGAUACCCUAAACAAAGGGUAUUC__AAAA
..((((((..((((((((.........)))))(((.....)))..........................))).))))))((((((((......))))))))....... (-23.30 = -23.25 +  -0.05)

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 09:37:13 2006