Locus 4323

Sequence ID 3L_DroMel_CAF1
Location 12,704,641 – 12,704,923
Length 282
Max. P 0.999818
window6685 window6686 window6687 window6688 window6689 window6690 window6691

overview

Window 5

Location 12,704,641 – 12,704,735
Length 94
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 95.28
Mean single sequence MFE -14.68
Consensus MFE -14.28
Energy contribution -14.28
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.23
Structure conservation index 0.97
SVM decision value 0.88
SVM RNA-class probability 0.873857
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12704641 94 - 23771897
AUCUGCUUAAGAUAGGAGAGAAAAUAAAAUAAAAUCCACUGGGUACAACCAAAUUAAUUUUGACAUAAUGUCAGACAAACAAAUGUUUGCACUU
.(((.((......)).)))....................(((......))).......((((((.....))))))(((((....)))))..... ( -14.60)
>DroSec_CAF1 68283 94 - 1
AUCUGCUUAAGAUAGGAGAGAAAAUGAAAUAAAAUCCACUGGGUACAACCAAAUUAAUUUUGACAUAAUGUCAGACAAACAAAUGUUUGCACUU
.(((.((......)).)))....................(((......))).......((((((.....))))))(((((....)))))..... ( -14.60)
>DroSim_CAF1 67036 94 - 1
AUCUGCUUAAGAUAGGAGAGAAAAUGAAAUAAAAUCCACUGGGUACAACCAAAUUAAUUUUGACAUAAUGUCAGACAAACAAAUGUUUGCACUU
.(((.((......)).)))....................(((......))).......((((((.....))))))(((((....)))))..... ( -14.60)
>DroEre_CAF1 70377 87 - 1
AUCUGCUUAAGAUAGGAGA-------AAAUAAAAUCCACUGGGUACAACCAAAUUAAUUUUGACAUAAUGUCAGACAAACAAAUGUUUGCACUU
((((.....)))).(((..-------........)))..(((......))).......((((((.....))))))(((((....)))))..... ( -14.80)
>DroYak_CAF1 70957 87 - 1
AUCUGCUUAAGAUAGGAGA-------AAAUAAAAUCCACUGGGUACAACCAAAUUAAUUUUGACAUAAUGUCAGACAAACAAAUGUUUGCACUU
((((.....)))).(((..-------........)))..(((......))).......((((((.....))))))(((((....)))))..... ( -14.80)
>consensus
AUCUGCUUAAGAUAGGAGAGAAAAU_AAAUAAAAUCCACUGGGUACAACCAAAUUAAUUUUGACAUAAUGUCAGACAAACAAAUGUUUGCACUU
.(((.((......)).)))....................(((......))).......((((((.....))))))(((((....)))))..... (-14.28 = -14.28 +   0.00)

alignment

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secondary structure

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Window 6

Location 12,704,655 – 12,704,764
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 95.38
Mean single sequence MFE -15.18
Consensus MFE -14.83
Energy contribution -14.83
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.43
Structure conservation index 0.98
SVM decision value 1.67
SVM RNA-class probability 0.971008
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12704655 109 - 23771897
AAACGAAUCGCAAAAUUAACAAGAUAAGCAUCUGCUUAAGAUAGGAGAGAAAAUAAAAUAAAAUCCACUGGGUACAACCAAAUUAAUUUUGACAUAAUGUCAGACAAAC
.........((((((((((.....(((((....))))).....(((.................)))..(((......)))..))))))))).)................ ( -14.83)
>DroSec_CAF1 68297 109 - 1
AAACGAAUCGCAAAAUUAACAAGAUAAGCAUCUGCUUAAGAUAGGAGAGAAAAUGAAAUAAAAUCCACUGGGUACAACCAAAUUAAUUUUGACAUAAUGUCAGACAAAC
.........((((((((((.....(((((....))))).....(((.................)))..(((......)))..))))))))).)................ ( -14.83)
>DroSim_CAF1 67050 109 - 1
AAACGAAUCGCAAAAUUAACAAGAUAAGCAUCUGCUUAAGAUAGGAGAGAAAAUGAAAUAAAAUCCACUGGGUACAACCAAAUUAAUUUUGACAUAAUGUCAGACAAAC
.........((((((((((.....(((((....))))).....(((.................)))..(((......)))..))))))))).)................ ( -14.83)
>DroEre_CAF1 70391 102 - 1
AAAUGAAUCGCAAAAUUAACAAGAUAAGCAUCUGCUUAAGAUAGGAGA-------AAAUAAAAUCCACUGGGUACAACCAAAUUAAUUUUGACAUAAUGUCAGACAAAC
...(((....(((((((((.....(((((....))))).....(((..-------........)))..(((......)))..)))))))))........)))....... ( -15.70)
>DroYak_CAF1 70971 102 - 1
AAAUGAAUCGCAAAAUUAACAAGAUAAGCAUCUGCUUAAGAUAGGAGA-------AAAUAAAAUCCACUGGGUACAACCAAAUUAAUUUUGACAUAAUGUCAGACAAAC
...(((....(((((((((.....(((((....))))).....(((..-------........)))..(((......)))..)))))))))........)))....... ( -15.70)
>consensus
AAACGAAUCGCAAAAUUAACAAGAUAAGCAUCUGCUUAAGAUAGGAGAGAAAAU_AAAUAAAAUCCACUGGGUACAACCAAAUUAAUUUUGACAUAAUGUCAGACAAAC
.........((((((((((.....(((((....))))).....(((.................)))..(((......)))..))))))))).)................ (-14.83 = -14.83 +   0.00)

alignment

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secondary structure

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Window 7

Location 12,704,735 – 12,704,843
Length 108
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 97.79
Mean single sequence MFE -23.90
Consensus MFE -21.19
Energy contribution -20.79
Covariance contribution -0.40
Combinations/Pair 1.11
Mean z-score -2.26
Structure conservation index 0.89
SVM decision value 2.38
SVM RNA-class probability 0.993172
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12704735 108 - 23771897
AAUCGAAAAUGCAUGCCGCGGCCUGAUCAAAAUAAAUUAUAAAACAAAAAGGGCCGCGCUCCGCAUUGGGU-UUGCCAUAAAACGAAUCGCAAAAUUAACAAGAUAAGC
.(((...(((((..((.(((((((..........................)))))))))...))))).(((-(((........)))))).............))).... ( -24.57)
>DroSec_CAF1 68377 108 - 1
AAUCGAAAAUGCAUGCCGCGGCCAGAUCAAAAUAAAUUAUAAAACAAAAAGGGCCGCGCUCCGCAUUGGGU-UUGCCAUAAAACGAAUCGCAAAAUUAACAAGAUAAGC
.(((...(((((..((.((((((............................))))))))...))))).(((-(((........)))))).............))).... ( -22.99)
>DroSim_CAF1 67130 108 - 1
AAUCGAAAAUGCAUGCCGCGGCCAGAUCAAAAUAAAUUAUAAAACAAAAAGGGCCGCGCUCCGCAUUGGGU-UUGCUAUAAAACGAAUCGCAAAAUUAACAAGAUAAGC
.(((...(((((..((.((((((............................))))))))...))))).(((-(((........)))))).............))).... ( -22.99)
>DroEre_CAF1 70464 108 - 1
AAUCGAAAAUGCAUGCCGCGGCCUGAUCAAAAUAAAUUAUAAAACAAAAAGGGCCGCGCUCCGCAUUGGGA-UUGCCAUAAAAUGAAUCGCAAAAUUAACAAGAUAAGC
.(((...(((((..((.(((((((..........................)))))))))...)))))(.((-((...........)))).)...........))).... ( -22.77)
>DroYak_CAF1 71044 109 - 1
AAUCGAAAAUGCAUGCCGCGGCCUGAUCAAAAUAAAUUAUAAAACAAAAAGGGCCGCGCUCCGCAUUGGGUUUUGCCAUAAAAUGAAUCGCAAAAUUAACAAGAUAAGC
.(((...(((((..((.(((((((..........................)))))))))...))))).((((((((.((.......)).)))))))).....))).... ( -26.17)
>consensus
AAUCGAAAAUGCAUGCCGCGGCCUGAUCAAAAUAAAUUAUAAAACAAAAAGGGCCGCGCUCCGCAUUGGGU_UUGCCAUAAAACGAAUCGCAAAAUUAACAAGAUAAGC
..(((..(((((..((.((((((............................))))))))...))))).((.....))......)))....................... (-21.19 = -20.79 +  -0.40)

alignment

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secondary structure

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Window 8

Location 12,704,764 – 12,704,883
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.32
Mean single sequence MFE -32.95
Consensus MFE -30.69
Energy contribution -30.77
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -1.57
Structure conservation index 0.93
SVM decision value 1.41
SVM RNA-class probability 0.951447
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12704764 119 + 23771897
UAUGGCAA-ACCCAAUGCGGAGCGCGGCCCUUUUUGUUUUAUAAUUUAUUUUGAUCAGGCCGCGGCAUGCAUUUUCGAUUGAUAUUGAUGGUUCCUUCUGGAGGAACAUGUUUUGCUCAU
.(((((((-(...((((((...(((((((............................)))))))...)))))).(((((....)))))..(((((((...)))))))....))))).))) ( -33.09)
>DroSec_CAF1 68406 119 + 1
UAUGGCAA-ACCCAAUGCGGAGCGCGGCCCUUUUUGUUUUAUAAUUUAUUUUGAUCUGGCCGCGGCAUGCAUUUUCGAUUGAUAUUGAUGGUUCCUUCUGGAGGAACAUGUUUUGCUCAU
.(((((((-(...((((((...(((((((...((.....((.....))....))...)))))))...)))))).(((((....)))))..(((((((...)))))))....))))).))) ( -32.90)
>DroSim_CAF1 67159 119 + 1
UAUAGCAA-ACCCAAUGCGGAGCGCGGCCCUUUUUGUUUUAUAAUUUAUUUUGAUCUGGCCGCGGCAUGCAUUUUCGAUUGAUAUUGAUGGUUCCUUCUGGAGGAACAUGUUUUGCUCAU
...(((((-(...((((((...(((((((...((.....((.....))....))...)))))))...)))))).(((((....)))))..(((((((...)))))))....))))))... ( -32.40)
>DroEre_CAF1 70493 119 + 1
UAUGGCAA-UCCCAAUGCGGAGCGCGGCCCUUUUUGUUUUAUAAUUUAUUUUGAUCAGGCCGCGGCAUGCAUUUUCGAUUGAUAUUGAUGGUUCCUUCUGCAGGAACAUGUUUUGCUCAU
.(((((((-..(.((((((...(((((((............................)))))))...)))))).(((((....)))))..((((((.....))))))..)..)))).))) ( -32.39)
>DroYak_CAF1 71073 120 + 1
UAUGGCAAAACCCAAUGCGGAGCGCGGCCCUUUUUGUUUUAUAAUUUAUUUUGAUCAGGCCGCGGCAUGCAUUUUCGAUUGAUAUUGAUGGUUCCUUCUGCGGAAACAUGUUUUGCUCAU
.((((((((((((((((((...(((((((............................)))))))...)))))..(((((....))))))))((((......))))....))))))).))) ( -33.99)
>consensus
UAUGGCAA_ACCCAAUGCGGAGCGCGGCCCUUUUUGUUUUAUAAUUUAUUUUGAUCAGGCCGCGGCAUGCAUUUUCGAUUGAUAUUGAUGGUUCCUUCUGGAGGAACAUGUUUUGCUCAU
...(((((.((..((((((...(((((((............................)))))))...)))))).(((((....)))))..((((((.....))))))..)).)))))... (-30.69 = -30.77 +   0.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,704,764 – 12,704,883
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.32
Mean single sequence MFE -32.32
Consensus MFE -29.65
Energy contribution -29.73
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -3.17
Structure conservation index 0.92
SVM decision value 4.16
SVM RNA-class probability 0.999818
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12704764 119 - 23771897
AUGAGCAAAACAUGUUCCUCCAGAAGGAACCAUCAAUAUCAAUCGAAAAUGCAUGCCGCGGCCUGAUCAAAAUAAAUUAUAAAACAAAAAGGGCCGCGCUCCGCAUUGGGU-UUGCCAUA
(((.(((((.(..((((((.....)))))).................(((((..((.(((((((..........................)))))))))...))))).).)-))))))). ( -32.07)
>DroSec_CAF1 68406 119 - 1
AUGAGCAAAACAUGUUCCUCCAGAAGGAACCAUCAAUAUCAAUCGAAAAUGCAUGCCGCGGCCAGAUCAAAAUAAAUUAUAAAACAAAAAGGGCCGCGCUCCGCAUUGGGU-UUGCCAUA
(((.(((((.(..((((((.....)))))).................(((((..((.((((((............................))))))))...))))).).)-))))))). ( -30.49)
>DroSim_CAF1 67159 119 - 1
AUGAGCAAAACAUGUUCCUCCAGAAGGAACCAUCAAUAUCAAUCGAAAAUGCAUGCCGCGGCCAGAUCAAAAUAAAUUAUAAAACAAAAAGGGCCGCGCUCCGCAUUGGGU-UUGCUAUA
...((((((.(..((((((.....)))))).................(((((..((.((((((............................))))))))...))))).).)-)))))... ( -30.29)
>DroEre_CAF1 70493 119 - 1
AUGAGCAAAACAUGUUCCUGCAGAAGGAACCAUCAAUAUCAAUCGAAAAUGCAUGCCGCGGCCUGAUCAAAAUAAAUUAUAAAACAAAAAGGGCCGCGCUCCGCAUUGGGA-UUGCCAUA
(((.((((..(..((((((.....)))))).................(((((..((.(((((((..........................)))))))))...))))).)..-))))))). ( -33.37)
>DroYak_CAF1 71073 120 - 1
AUGAGCAAAACAUGUUUCCGCAGAAGGAACCAUCAAUAUCAAUCGAAAAUGCAUGCCGCGGCCUGAUCAAAAUAAAUUAUAAAACAAAAAGGGCCGCGCUCCGCAUUGGGUUUUGCCAUA
(((.((((((((((.((((......)))).)))..............(((((..((.(((((((..........................)))))))))...)))))..)))))))))). ( -35.37)
>consensus
AUGAGCAAAACAUGUUCCUCCAGAAGGAACCAUCAAUAUCAAUCGAAAAUGCAUGCCGCGGCCUGAUCAAAAUAAAUUAUAAAACAAAAAGGGCCGCGCUCCGCAUUGGGU_UUGCCAUA
(((.((((.((..((((((.....)))))).................(((((..((.((((((............................))))))))...)))))..)).))))))). (-29.65 = -29.73 +   0.08)

alignment

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secondary structure

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dotplot

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Window 0

Location 12,704,803 – 12,704,923
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.83
Mean single sequence MFE -29.82
Consensus MFE -27.92
Energy contribution -28.36
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.26
Structure conservation index 0.94
SVM decision value 0.29
SVM RNA-class probability 0.670300
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12704803 120 + 23771897
AUAAUUUAUUUUGAUCAGGCCGCGGCAUGCAUUUUCGAUUGAUAUUGAUGGUUCCUUCUGGAGGAACAUGUUUUGCUCAUCAAUGAAUUGGCGCUGAACCUGUUUGCCCUGCCUCAUUUA
............(((.((((.(.((((.(((..((((.(..((((((((((((((((...)))))))..(.....).)))))))..))..)...))))..))).))))).)))).))).. ( -30.70)
>DroSec_CAF1 68445 120 + 1
AUAAUUUAUUUUGAUCUGGCCGCGGCAUGCAUUUUCGAUUGAUAUUGAUGGUUCCUUCUGGAGGAACAUGUUUUGCUCAUCAAUGAAUUGGCGCUGAACCUGUUUGCCCUGCCUCAUUUA
.................(((.(.((((.(((..((((.(..((((((((((((((((...)))))))..(.....).)))))))..))..)...))))..))).))))).)))....... ( -29.30)
>DroSim_CAF1 67198 120 + 1
AUAAUUUAUUUUGAUCUGGCCGCGGCAUGCAUUUUCGAUUGAUAUUGAUGGUUCCUUCUGGAGGAACAUGUUUUGCUCAUCAAUGAAUUGGCGCUGAACCUGUUUGCCCUGCCUCAUUUA
.................(((.(.((((.(((..((((.(..((((((((((((((((...)))))))..(.....).)))))))..))..)...))))..))).))))).)))....... ( -29.30)
>DroEre_CAF1 70532 120 + 1
AUAAUUUAUUUUGAUCAGGCCGCGGCAUGCAUUUUCGAUUGAUAUUGAUGGUUCCUUCUGCAGGAACAUGUUUUGCUCAUCAAUGAAUUGGCUCUGAACCUGUUUGCCCUGCCUCAUUUA
............(((.((((.(.((((.(((..((((((..(((((((((((((((.....))))))..(.....).)))))))..))..).)).)))..))).))))).)))).))).. ( -31.40)
>DroYak_CAF1 71113 120 + 1
AUAAUUUAUUUUGAUCAGGCCGCGGCAUGCAUUUUCGAUUGAUAUUGAUGGUUCCUUCUGCGGAAACAUGUUUUGCUCAUCAAUGAAUUGGCUCUGAACCUGUUUGCCCUGCCUCAUUUA
............(((.((((.(.((((.(((..((((((..((((((((((((((......)))).((.....)).))))))))..))..).)).)))..))).))))).)))).))).. ( -28.40)
>consensus
AUAAUUUAUUUUGAUCAGGCCGCGGCAUGCAUUUUCGAUUGAUAUUGAUGGUUCCUUCUGGAGGAACAUGUUUUGCUCAUCAAUGAAUUGGCGCUGAACCUGUUUGCCCUGCCUCAUUUA
............(((.((((.(.((((.(((..((((.(..(((((((((((((((.....))))))..(.....).)))))))..))..)...))))..))).))))).)))).))).. (-27.92 = -28.36 +   0.44)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,704,803 – 12,704,923
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.83
Mean single sequence MFE -27.36
Consensus MFE -24.76
Energy contribution -24.80
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.66
Structure conservation index 0.90
SVM decision value 1.25
SVM RNA-class probability 0.936557
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12704803 120 - 23771897
UAAAUGAGGCAGGGCAAACAGGUUCAGCGCCAAUUCAUUGAUGAGCAAAACAUGUUCCUCCAGAAGGAACCAUCAAUAUCAAUCGAAAAUGCAUGCCGCGGCCUGAUCAAAAUAAAUUAU
...((.((((.(((((..(((((.....))).....(((((((..........((((((.....)))))))))))))............))..)))).).)))).))............. ( -27.30)
>DroSec_CAF1 68445 120 - 1
UAAAUGAGGCAGGGCAAACAGGUUCAGCGCCAAUUCAUUGAUGAGCAAAACAUGUUCCUCCAGAAGGAACCAUCAAUAUCAAUCGAAAAUGCAUGCCGCGGCCAGAUCAAAAUAAAUUAU
.......(((.(((((..(((((.....))).....(((((((..........((((((.....)))))))))))))............))..)))).).)))................. ( -25.70)
>DroSim_CAF1 67198 120 - 1
UAAAUGAGGCAGGGCAAACAGGUUCAGCGCCAAUUCAUUGAUGAGCAAAACAUGUUCCUCCAGAAGGAACCAUCAAUAUCAAUCGAAAAUGCAUGCCGCGGCCAGAUCAAAAUAAAUUAU
.......(((.(((((..(((((.....))).....(((((((..........((((((.....)))))))))))))............))..)))).).)))................. ( -25.70)
>DroEre_CAF1 70532 120 - 1
UAAAUGAGGCAGGGCAAACAGGUUCAGAGCCAAUUCAUUGAUGAGCAAAACAUGUUCCUGCAGAAGGAACCAUCAAUAUCAAUCGAAAAUGCAUGCCGCGGCCUGAUCAAAAUAAAUUAU
...((.((((.(((((..((..(((.(((....)))(((((((..........((((((.....))))))))))))).......)))..))..)))).).)))).))............. ( -30.10)
>DroYak_CAF1 71113 120 - 1
UAAAUGAGGCAGGGCAAACAGGUUCAGAGCCAAUUCAUUGAUGAGCAAAACAUGUUUCCGCAGAAGGAACCAUCAAUAUCAAUCGAAAAUGCAUGCCGCGGCCUGAUCAAAAUAAAUUAU
...((.((((.(((((..((..(((.(((....)))(((((((((((.....))))(((......)))..))))))).......)))..))..)))).).)))).))............. ( -28.00)
>consensus
UAAAUGAGGCAGGGCAAACAGGUUCAGCGCCAAUUCAUUGAUGAGCAAAACAUGUUCCUCCAGAAGGAACCAUCAAUAUCAAUCGAAAAUGCAUGCCGCGGCCUGAUCAAAAUAAAUUAU
.......(((.(((((..(((((.....))).....(((((((..........((((((.....)))))))))))))............))..)))).).)))................. (-24.76 = -24.80 +   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 11:19:35 2006