Locus 1922

Sequence ID 2L_DroMel_CAF1
Location 5,229,704 – 5,230,055
Length 351
Max. P 0.998033
window3100 window3101 window3102 window3103 window3104

overview

Window 0

Location 5,229,704 – 5,229,824
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.35
Mean single sequence MFE -22.84
Consensus MFE -19.47
Energy contribution -20.04
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -1.69
Structure conservation index 0.85
SVM decision value 0.48
SVM RNA-class probability 0.751073
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5229704 120 + 22407834
AAAAAUCUUAUCGGCCAGCGACUUUAAUGUCGGACAUUGAAUUACAGCUCGAGAGCAAAAAAAAAAGAGAUAUAUAAGACACAAUUUGCAUAAUUCAAUGGCAGCAGCAGCUGAUAUAAU
........(((((((...((((......))))..((((((((((..(((....))).....................(.((.....))).))))))))))((....)).))))))).... ( -25.60)
>DroSec_CAF1 7086 119 + 1
ACAAAUCUUAUCGGACAGCGACUUUAAUGUCGGACAUUGAAUUACAGUUCGAGAGCAAAAAA-AAAAAUAUAUAUAAGAAACAAUUUGCAUAAUUCAAUGGCAGCAGCAGCUGAUAUAAU
........((((((...(((((......)))...(((((((((((.....)...(((((...-.....................))))).))))))))))......))..)))))).... ( -21.16)
>DroSim_CAF1 7999 119 + 1
AAAAAUCUUAUCGGCCAGCGACUUUAAUGUCGGACAUUGAAUUACAGUUCGAGACCAAAAAA-AGAGAUAUAUAUAAGAAACAAUUUGCAUAAUUCAAUGGCAGCAGCAGCUGAUAUAAU
........(((((((...((((......))))..(((((((((((((...............-......................)))..))))))))))((....)).))))))).... ( -21.29)
>DroYak_CAF1 8878 120 + 1
AAAAAUCUUAUCGGCCAACGACUUUGAUGGCGGACAUUGAAUUACCGAUCGAGAGCAGAAAAAAAAAAAUUAUAUAAGACAAAAUUUGCAUAAUUCAAUGGCAGCAGCAGCUGAUAUAAU
..........((.((((.((....)).)))).))((((((((((.(......).(((((.........................))))).)))))))))).((((....))))....... ( -23.31)
>consensus
AAAAAUCUUAUCGGCCAGCGACUUUAAUGUCGGACAUUGAAUUACAGUUCGAGAGCAAAAAA_AAAAAUAUAUAUAAGAAACAAUUUGCAUAAUUCAAUGGCAGCAGCAGCUGAUAUAAU
........(((((((...((((......))))..(((((((((((.....)...(((((.........................))))).))))))))))((....)).))))))).... (-19.47 = -20.04 +   0.56)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,229,744 – 5,229,864
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.02
Mean single sequence MFE -19.93
Consensus MFE -17.15
Energy contribution -17.27
Covariance contribution 0.13
Combinations/Pair 1.14
Mean z-score -1.49
Structure conservation index 0.86
SVM decision value 0.01
SVM RNA-class probability 0.536216
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5229744 120 + 22407834
AUUACAGCUCGAGAGCAAAAAAAAAAGAGAUAUAUAAGACACAAUUUGCAUAAUUCAAUGGCAGCAGCAGCUGAUAUAAUUUUUAUUGCGAUUUUAUCAAGAAAUCGAAAAUGAGCAAAC
......(((((...((((.(((((..(((.(((.((((......)))).))).))).(((.((((....)))).)))..))))).))))((((((.....)))))).....))))).... ( -22.70)
>DroSec_CAF1 7126 119 + 1
AUUACAGUUCGAGAGCAAAAAA-AAAAAUAUAUAUAAGAAACAAUUUGCAUAAUUCAAUGGCAGCAGCAGCUGAUAUAAUUUUUAUUGCGAUUUUAUCAAGAAAUCGAAAAUGAGCAAAC
......(((((...((((.(((-((..((((.................(((......))).((((....))))))))..))))).))))((((((.....)))))).....))))).... ( -19.80)
>DroSim_CAF1 8039 119 + 1
AUUACAGUUCGAGACCAAAAAA-AGAGAUAUAUAUAAGAAACAAUUUGCAUAAUUCAAUGGCAGCAGCAGCUGAUAUAAUUUUUAUUGCGAUUUUAUCAAGAAAUCGAAAAUGAGCAAAA
......(((((...........-((((((.(((((.............(((......))).((((....)))))))))))))))....(((((((.....)))))))....))))).... ( -17.90)
>DroYak_CAF1 8918 120 + 1
AUUACCGAUCGAGAGCAGAAAAAAAAAAAUUAUAUAAGACAAAAUUUGCAUAAUUCAAUGGCAGCAGCAGCUGAUAUAAUUUUUAUUGCGAUUUUAUCAAGAAAUCGAAAAUGAGCAAAC
..............((........(((((((((((.............(((......))).((((....)))))))))))))))....(((((((.....))))))).......)).... ( -19.30)
>consensus
AUUACAGUUCGAGAGCAAAAAA_AAAAAUAUAUAUAAGAAACAAUUUGCAUAAUUCAAUGGCAGCAGCAGCUGAUAUAAUUUUUAUUGCGAUUUUAUCAAGAAAUCGAAAAUGAGCAAAC
......(((((.............(((((.(((((.............(((......))).((((....))))))))).)))))....(((((((.....)))))))....))))).... (-17.15 = -17.27 +   0.13)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,229,864 – 5,229,983
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.66
Mean single sequence MFE -34.43
Consensus MFE -28.80
Energy contribution -29.00
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.84
SVM decision value 1.15
SVM RNA-class probability 0.922117
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5229864 119 + 22407834
CGAAUCGGGGGAUCAAUGACAUUAAUAUUGAUAUUGGGGCGAUGAUUGCCAAUCAUCAUCGCC-GCAAGAUCGAAAUUGGAAUUGGAUUCGAAUGCAAAUCAGGAGGAGGCGUUAGCCAA
((((((.((...(((((..........(((((.(((.(((((((((........)))))))))-.))).))))).)))))..)).)))))).................(((....))).. ( -36.00)
>DroSec_CAF1 7245 120 + 1
CGAAUCGGGGGAUCAACGACAUUAAUAUUGAUAUUGGGGCGAUGAUUGCCAAUCAUCAACGCCAGCAAGAUCGAAAUUGGAUUUGGAUUCGAAUGCAAAUCAGGAGGAGGCGUUAGCCAA
(((((((..(......)..).(((((.(((((.(((.((((.((((........)))).))))..))).))))).))))).....)))))).................(((....))).. ( -29.70)
>DroSim_CAF1 8158 120 + 1
CGAAUCGGGGGAUCAACGACAUUAAUAUUGAUAUUGGGGCGAUGAUUGCCAAUCAUCAUCGCCAGCAAGAUCGAAAUUGGAAUUGGAUUCGAAUGCAAAUCAGGAGGAGGCGUUAGCCAA
((((((((....))..(((..(((((.(((((.(((.(((((((((........)))))))))..))).))))).)))))..))))))))).................(((....))).. ( -34.60)
>DroEre_CAF1 11 119 + 1
CAAAUCGGAGGAUCAACGACAUUAAUAUUGAUAUUGGGGCGAUGAUUGCCAAUCAUCAUCGCC-GCAAGAUCGAAAUUGUAAUUGGAUUCGAAUGCAAAUCAGGAGGAGGCGUUAGCCAA
......((.(((((........((((.(((((.(((.(((((((((........)))))))))-.))).))))).))))......))))).(((((...((.....)).)))))..)).. ( -35.34)
>DroYak_CAF1 9038 119 + 1
CGAAUCGGGGGAUCAACGACAUUAAUAUUGAUAUUGGGGCGAUGAUUGCCAAUCAUCAUCGCC-GCAAGAUCGAAAUUGUAAUUGGAUUCGAAUGCAAAUCGGUAGGAGGCGUUAGCCAA
((((((((....))..(((...((((.(((((.(((.(((((((((........)))))))))-.))).))))).))))...)))))))))..(((......)))...(((....))).. ( -36.50)
>consensus
CGAAUCGGGGGAUCAACGACAUUAAUAUUGAUAUUGGGGCGAUGAUUGCCAAUCAUCAUCGCC_GCAAGAUCGAAAUUGGAAUUGGAUUCGAAUGCAAAUCAGGAGGAGGCGUUAGCCAA
......((.(((((........((((.(((((.....(((((((((........)))))))))......))))).))))......))))).(((((...((.....)).)))))..)).. (-28.80 = -29.00 +   0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,229,864 – 5,229,983
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.66
Mean single sequence MFE -29.31
Consensus MFE -27.08
Energy contribution -27.12
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -2.11
Structure conservation index 0.92
SVM decision value 2.99
SVM RNA-class probability 0.998033
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5229864 119 - 22407834
UUGGCUAACGCCUCCUCCUGAUUUGCAUUCGAAUCCAAUUCCAAUUUCGAUCUUGC-GGCGAUGAUGAUUGGCAAUCAUCGCCCCAAUAUCAAUAUUAAUGUCAUUGAUCCCCCGAUUCG
..(((....))).................((((((.............(((.(((.-(((((((((........))))))))).))).)))...((((((...)))))).....)))))) ( -30.80)
>DroSec_CAF1 7245 120 - 1
UUGGCUAACGCCUCCUCCUGAUUUGCAUUCGAAUCCAAAUCCAAUUUCGAUCUUGCUGGCGUUGAUGAUUGGCAAUCAUCGCCCCAAUAUCAAUAUUAAUGUCGUUGAUCCCCCGAUUCG
..(((.((((((............(((.(((((............)))))...))).))))))((((((.....))))))))).....((((((.........))))))........... ( -25.02)
>DroSim_CAF1 8158 120 - 1
UUGGCUAACGCCUCCUCCUGAUUUGCAUUCGAAUCCAAUUCCAAUUUCGAUCUUGCUGGCGAUGAUGAUUGGCAAUCAUCGCCCCAAUAUCAAUAUUAAUGUCGUUGAUCCCCCGAUUCG
..(((....))).................((((((.............(((.(((..(((((((((........))))))))).))).)))...((((((...)))))).....)))))) ( -29.40)
>DroEre_CAF1 11 119 - 1
UUGGCUAACGCCUCCUCCUGAUUUGCAUUCGAAUCCAAUUACAAUUUCGAUCUUGC-GGCGAUGAUGAUUGGCAAUCAUCGCCCCAAUAUCAAUAUUAAUGUCGUUGAUCCUCCGAUUUG
..(((....))).......((((((....))))))((((.(((.....(((.(((.-(((((((((........))))))))).))).)))........))).))))............. ( -30.22)
>DroYak_CAF1 9038 119 - 1
UUGGCUAACGCCUCCUACCGAUUUGCAUUCGAAUCCAAUUACAAUUUCGAUCUUGC-GGCGAUGAUGAUUGGCAAUCAUCGCCCCAAUAUCAAUAUUAAUGUCGUUGAUCCCCCGAUUCG
..(((....))).................((((((.............(((.(((.-(((((((((........))))))))).))).)))...((((((...)))))).....)))))) ( -31.10)
>consensus
UUGGCUAACGCCUCCUCCUGAUUUGCAUUCGAAUCCAAUUCCAAUUUCGAUCUUGC_GGCGAUGAUGAUUGGCAAUCAUCGCCCCAAUAUCAAUAUUAAUGUCGUUGAUCCCCCGAUUCG
..(((....)))............(((.(((((............)))))...))).(((((((((........))))))))).....((((((.........))))))........... (-27.08 = -27.12 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,229,943 – 5,230,055
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.49
Mean single sequence MFE -29.06
Consensus MFE -23.16
Energy contribution -23.20
Covariance contribution 0.04
Combinations/Pair 1.12
Mean z-score -2.36
Structure conservation index 0.80
SVM decision value 1.80
SVM RNA-class probability 0.977987
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5229943 112 - 22407834
AAAAGAAUGCUCCUCCAUUUCGCUACUGUGGAGCAAAUCGUCUG--------AUCAUCUUGAUCUCGGCUUGAGUGACUUUUGGCUAACGCCUCCUCCUGAUUUGCAUUCGAAUCCAAUU
....((((((..((((((.........)))))).((((((((.(--------(((.....))))..)))..(((.((.....(((....))))))))..))))))))))).......... ( -30.80)
>DroSec_CAF1 7325 112 - 1
AACAGAAUGCUCCUCCAUUUCGCUACUGUGGAGCAAAUCAUCUG--------GUCAUCACGAUCUCGGCUUGAGUGACUUUUGGCUAACGCCUCCUCCUGAUUUGCAUUCGAAUCCAAAU
....((((((..((((((.........)))))).((((((...(--------(((((((((....))...))).)))))...(((....)))......)))))))))))).......... ( -29.60)
>DroSim_CAF1 8238 112 - 1
AACAGAAUACUCCUCCAUUUCGCUACUGUGGAGCAAAUCAUCUG--------GUCAUCUUGAUCUCGGCUUGAGUGACUUUUGGCUAACGCCUCCUCCUGAUUUGCAUUCGAAUCCAAUU
....((((.....(((((.........)))))((((((((...(--------((((.((..(.......)..)))))))...(((....)))......)))))))))))).......... ( -28.70)
>DroEre_CAF1 90 120 - 1
AAAAGAAUGCUCCUCCAUUUCGCUACUGUGGAGCAAAUCAUCUGAUCAUCUGAUCAUCUUGAUUUCAGCUUGAGUGACUUUUGGCUAACGCCUCCUCCUGAUUUGCAUUCGAAUCCAAUU
....((((((..((((((.........))))))..(((((..(((((....)))))...)))))((((...(((.((.....(((....))))))))))))...)))))).......... ( -32.10)
>DroYak_CAF1 9117 112 - 1
AUAAGUAUGCUCCUUCAUUUCGCUACUGUGGAGCAAAUCAUCUG--------AUCAUUUUGAUCUCAGCUUGAGUGACUUUUGGCUAACGCCUCCUACCGAUUUGCAUUCGAAUCCAAUU
.............(((..(((((....)))))(((((((.((..--------.(((..(((....)))..)))..)).....(((....))).......)))))))....)))....... ( -24.10)
>consensus
AAAAGAAUGCUCCUCCAUUUCGCUACUGUGGAGCAAAUCAUCUG________AUCAUCUUGAUCUCGGCUUGAGUGACUUUUGGCUAACGCCUCCUCCUGAUUUGCAUUCGAAUCCAAUU
....((((((..((((((.........)))))).(((((..............(((..(((....)))..))).........(((....))).......))))))))))).......... (-23.16 = -23.20 +   0.04)

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 10:14:56 2006