Locus 6751

Sequence ID X_DroMel_CAF1
Location 16,767,786 – 16,768,003
Length 217
Max. P 0.923384
window11044 window11045 window11046 window11047 window11048 window11049

overview

Window 4

Location 16,767,786 – 16,767,901
Length 115
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 96.51
Mean single sequence MFE -12.29
Consensus MFE -11.82
Energy contribution -12.15
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.62
Structure conservation index 0.96
SVM decision value 0.25
SVM RNA-class probability 0.653704
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16767786 115 + 22224390
AAAACUAAAAACCAAUAACUUAAAACUAAUUACAUUAUUAAGCAACUUUUUCCUCAGCUUCAUUAAUUUCCCAAAAUUUAUCGCACAUCAUUGCUCGAAUGAUGUGUUAUCGAUA
.................................((((..((((.............))))...))))...........((((((((((((((.....)))))))))....))))) ( -13.72)
>DroSec_CAF1 5206 114 + 1
UAAACUAAAUACCAAUAACUUAAAACUAAUUACAUUAUUAAGCAACUUUUUCCUCAGCUUCAUUAAUUUCCCAAA-UUUAUCGCACAUCAUUUCUCGAAUGAUGUGUUAUCGAUA
.................................((((..((((.............))))...))))........-..(((((((((((((((...))))))))))....))))) ( -13.72)
>DroSim_CAF1 5130 113 + 1
UAAACUAAAUACCAAUAACUUAAAACUAAUUACAUUAUUAAGCAACUUUUUCCUCAGCUUCAUUAAUUUCCCAAA-U-UAUCGCCCAUCAUUGCUCGAAUGAUGUGUUAUCGAUA
............(.(((((..............((((..((((.............))))...))))........-.-.......(((((((.....))))))).))))).)... (  -9.42)
>consensus
UAAACUAAAUACCAAUAACUUAAAACUAAUUACAUUAUUAAGCAACUUUUUCCUCAGCUUCAUUAAUUUCCCAAA_UUUAUCGCACAUCAUUGCUCGAAUGAUGUGUUAUCGAUA
.................................((((..((((.............))))...))))...........((((((((((((((.....)))))))))....))))) (-11.82 = -12.15 +   0.33)

alignment

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secondary structure

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Window 5

Location 16,767,786 – 16,767,901
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 96.51
Mean single sequence MFE -23.73
Consensus MFE -20.90
Energy contribution -21.23
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.80
Structure conservation index 0.88
SVM decision value -0.05
SVM RNA-class probability 0.507489
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16767786 115 - 22224390
UAUCGAUAACACAUCAUUCGAGCAAUGAUGUGCGAUAAAUUUUGGGAAAUUAAUGAAGCUGAGGAAAAAGUUGCUUAAUAAUGUAAUUAGUUUUAAGUUAUUGGUUUUUAGUUUU
(((((....(((((((((.....)))))))))))))).................(((((((((((...(((.((((((...((....))...)))))).)))..))))))))))) ( -25.60)
>DroSec_CAF1 5206 114 - 1
UAUCGAUAACACAUCAUUCGAGAAAUGAUGUGCGAUAAA-UUUGGGAAAUUAAUGAAGCUGAGGAAAAAGUUGCUUAAUAAUGUAAUUAGUUUUAAGUUAUUGGUAUUUAGUUUA
((((((((((((((((((.....))))))))........-.............((((((((........(((((........))))))))))))).))))))))))......... ( -23.30)
>DroSim_CAF1 5130 113 - 1
UAUCGAUAACACAUCAUUCGAGCAAUGAUGGGCGAUA-A-UUUGGGAAAUUAAUGAAGCUGAGGAAAAAGUUGCUUAAUAAUGUAAUUAGUUUUAAGUUAUUGGUAUUUAGUUUA
((((((((((.(((((((.....))))))).......-.-.............((((((((........(((((........))))))))))))).))))))))))......... ( -22.30)
>consensus
UAUCGAUAACACAUCAUUCGAGCAAUGAUGUGCGAUAAA_UUUGGGAAAUUAAUGAAGCUGAGGAAAAAGUUGCUUAAUAAUGUAAUUAGUUUUAAGUUAUUGGUAUUUAGUUUA
((((((((((.(((((((.....))))))).......................((((((((........(((((........))))))))))))).))))))))))......... (-20.90 = -21.23 +   0.33)

alignment

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secondary structure

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Window 6

Location 16,767,824 – 16,767,941
Length 117
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 84.88
Mean single sequence MFE -23.40
Consensus MFE -14.45
Energy contribution -15.95
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.96
Structure conservation index 0.62
SVM decision value 1.14
SVM RNA-class probability 0.920796
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16767824 117 + 22224390
UAAGCAACUUUUUCCUCAGCUUCAUUAAUUUCCCAAAAUUUAUCGCACAUCAUU-GCUCGAAUGAUGUGUUAUCGAUAAAUUCGAAAUACGAAAUUCGAAAAACGGCUUGCAGAGCAA
(((((...((((((.............(((((....((((((((((((((((((-.....)))))))))....))))))))).)))))..(.....)))))))..)))))........ ( -24.80)
>DroSec_CAF1 5244 115 + 1
UAAGCAACUUUUUCCUCAGCUUCAUUAAUUUCCCAAA-UUUAUCGCACAUCAUU-UCUCGAAUGAUGUGUUAUCGAUAAAUUCGAUAUUCGAAAUUCAAAAAGC-GCUUGCAGAGCAA
..................((((....((((((.....-......((((((((((-(...)))))))))))((((((.....))))))...))))))....))))-((((...)))).. ( -26.80)
>DroSim_CAF1 5168 114 + 1
UAAGCAACUUUUUCCUCAGCUUCAUUAAUUUCCCAAA-U-UAUCGCCCAUCAUU-GCUCGAAUGAUGUGUUAUCGAUAAAUUCGAUAUUCGAAAUUCAAAAAGC-GCUUGCAGAGCAA
..................((((....((((((.....-.-....((.(((((((-.....))))))).))((((((.....))))))...))))))....))))-((((...)))).. ( -22.00)
>DroEre_CAF1 8160 99 + 1
UAAGCAACUUUUUCCUCAGCUUUAUUAAUUUCCCAA-AUUUAUCGCACAUCAUUCACUCGAAUGCU--GUUCUCGAUAAAUUCGAAAUGCA----------------CUCCAGAGCAA
..................(((((....(((((...(-((((((((.(((.(((((....))))).)--))...))))))))).)))))...----------------....))))).. ( -20.00)
>consensus
UAAGCAACUUUUUCCUCAGCUUCAUUAAUUUCCCAAA_UUUAUCGCACAUCAUU_GCUCGAAUGAUGUGUUAUCGAUAAAUUCGAAAUUCGAAAUUCAAAAAGC_GCUUGCAGAGCAA
..................((((......................((((((((((......))))))))))((((((.....)))))).........................)))).. (-14.45 = -15.95 +   1.50)

alignment

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secondary structure

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Window 7

Location 16,767,864 – 16,767,967
Length 103
Sequences 4
Columns 104
Reading direction forward
Mean pairwise identity 84.95
Mean single sequence MFE -20.75
Consensus MFE -13.05
Energy contribution -14.55
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.04
Structure conservation index 0.63
SVM decision value 0.32
SVM RNA-class probability 0.687202
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16767864 103 + 22224390
UAUCGCACAUCAUU-GCUCGAAUGAUGUGUUAUCGAUAAAUUCGAAAUACGAAAUUCGAAAAACGGCUUGCAGAGCAACAGCCAUGAGCUAACCAAACUCUCCC
((((((((((((((-.....)))))))))....)))))..((((((........))))))....(((((((...)))..))))..(((.........))).... ( -24.50)
>DroSec_CAF1 5283 102 + 1
UAUCGCACAUCAUU-UCUCGAAUGAUGUGUUAUCGAUAAAUUCGAUAUUCGAAAUUCAAAAAGC-GCUUGCAGAGCAACAGCCAUGAGCUAACCAAACUCUCCC
..((((((((((((-(...)))))))))))((((((.....))))))...)).........(((-((((...))))..((....)).))).............. ( -22.40)
>DroSim_CAF1 5206 102 + 1
UAUCGCCCAUCAUU-GCUCGAAUGAUGUGUUAUCGAUAAAUUCGAUAUUCGAAAUUCAAAAAGC-GCUUGCAGAGCAACAGCCAUGAGCUAACCAAACUCUCCC
....((.(((..((-((((((((..((...((((((.....))))))..))..)))).....((-....)).)))))).....))).))............... ( -21.30)
>DroEre_CAF1 8199 86 + 1
UAUCGCACAUCAUUCACUCGAAUGCU--GUUCUCGAUAAAUUCGAAAUGCA----------------CUCCAGAGCAACAGCCAUGAGCUAACCAAACUCUCCC
....((.(((.((((....))))(((--((..((((.....))))..(((.----------------.......)))))))).))).))............... ( -14.80)
>consensus
UAUCGCACAUCAUU_GCUCGAAUGAUGUGUUAUCGAUAAAUUCGAAAUUCGAAAUUCAAAAAGC_GCUUGCAGAGCAACAGCCAUGAGCUAACCAAACUCUCCC
....((((((((((......))))))))))((((((.....))))))........................((((....(((.....))).......))))... (-13.05 = -14.55 +   1.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,767,901 – 16,768,003
Length 102
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 87.52
Mean single sequence MFE -19.38
Consensus MFE -15.15
Energy contribution -15.40
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.78
SVM decision value 0.71
SVM RNA-class probability 0.828896
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16767901 102 + 22224390
AAUUCGAAAUACGAAAUUCGAAAAACGGCUUGCAGAGCAACAGCCAUGAGCUAACCAAACUCUCCCAUUACAGGGCACGGCCAAUCUGCAAUCCUCUAUAAA
..((((((........))))))....((.(((((((......(((..(((.........))).(((......)))...)))...))))))).))........ ( -25.20)
>DroSec_CAF1 5320 101 + 1
AAUUCGAUAUUCGAAAUUCAAAAAGC-GCUUGCAGAGCAACAGCCAUGAGCUAACCAAACUCUCCCAUUCCAGGGCACGGCCAAUCUGCAAUCCUCUAUAAA
..((((.....))))........((.-(.(((((((......(((..(((.........))).(((......)))...)))...))))))).)))....... ( -20.40)
>DroSim_CAF1 5243 101 + 1
AAUUCGAUAUUCGAAAUUCAAAAAGC-GCUUGCAGAGCAACAGCCAUGAGCUAACCAAACUCUCCCAUUCCAGGGCACGGCCAAUCUGCAAUCCUCUAUAAA
..((((.....))))........((.-(.(((((((......(((..(((.........))).(((......)))...)))...))))))).)))....... ( -20.40)
>DroEre_CAF1 8235 86 + 1
AAUUCGAAAUGCA----------------CUCCAGAGCAACAGCCAUGAGCUAACCAAACUCUCCCAUUCUAGGGCACGGCCAAUCUGCAAUCCUCUAUAAA
.............----------------...((((......(((..(((.........))).(((......)))...)))...)))).............. ( -11.50)
>consensus
AAUUCGAAAUUCGAAAUUCAAAAAGC_GCUUGCAGAGCAACAGCCAUGAGCUAACCAAACUCUCCCAUUCCAGGGCACGGCCAAUCUGCAAUCCUCUAUAAA
..............................((((((......(((..(((.........))).(((......)))...)))...))))))............ (-15.15 = -15.40 +   0.25)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,767,901 – 16,768,003
Length 102
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 87.52
Mean single sequence MFE -30.85
Consensus MFE -24.65
Energy contribution -25.03
Covariance contribution 0.38
Combinations/Pair 1.08
Mean z-score -2.17
Structure conservation index 0.80
SVM decision value 1.15
SVM RNA-class probability 0.923384
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16767901 102 - 22224390
UUUAUAGAGGAUUGCAGAUUGGCCGUGCCCUGUAAUGGGAGAGUUUGGUUAGCUCAUGGCUGUUGCUCUGCAAGCCGUUUUUCGAAUUUCGUAUUUCGAAUU
........((.(((((((.(((((((.(((......))).(((((.....))))))))))))....))))))).))....((((((........)))))).. ( -34.30)
>DroSec_CAF1 5320 101 - 1
UUUAUAGAGGAUUGCAGAUUGGCCGUGCCCUGGAAUGGGAGAGUUUGGUUAGCUCAUGGCUGUUGCUCUGCAAGC-GCUUUUUGAAUUUCGAAUAUCGAAUU
((((.(((((.(((((((.(((((((.(((......))).(((((.....))))))))))))....))))))).)-.)))).)))).((((.....)))).. ( -32.10)
>DroSim_CAF1 5243 101 - 1
UUUAUAGAGGAUUGCAGAUUGGCCGUGCCCUGGAAUGGGAGAGUUUGGUUAGCUCAUGGCUGUUGCUCUGCAAGC-GCUUUUUGAAUUUCGAAUAUCGAAUU
((((.(((((.(((((((.(((((((.(((......))).(((((.....))))))))))))....))))))).)-.)))).)))).((((.....)))).. ( -32.10)
>DroEre_CAF1 8235 86 - 1
UUUAUAGAGGAUUGCAGAUUGGCCGUGCCCUAGAAUGGGAGAGUUUGGUUAGCUCAUGGCUGUUGCUCUGGAG----------------UGCAUUUCGAAUU
........(.(((.((((.(((((((.(((......))).(((((.....))))))))))))....)))).))----------------).).......... ( -24.90)
>consensus
UUUAUAGAGGAUUGCAGAUUGGCCGUGCCCUGGAAUGGGAGAGUUUGGUUAGCUCAUGGCUGUUGCUCUGCAAGC_GCUUUUUGAAUUUCGAAUAUCGAAUU
...........(((((((.(((((((.(((......))).(((((.....))))))))))))....)))))))..............((((.....)))).. (-24.65 = -25.03 +   0.38)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:59 2006