Locus 136

Sequence ID 2R_DroMel_CAF1
Location 1,398,309 – 1,398,506
Length 197
Max. P 0.986587
window288 window289 window290 window291 window292

overview

Window 8

Location 1,398,309 – 1,398,427
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.31
Mean single sequence MFE -32.28
Consensus MFE -26.26
Energy contribution -25.90
Covariance contribution -0.36
Combinations/Pair 1.17
Mean z-score -2.38
Structure conservation index 0.81
SVM decision value 2.05
SVM RNA-class probability 0.986587
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1398309 118 + 20766785
UUGACAAAUGGAAAUGUCAAAAUGAAAAAUUAACUGAAAAUCAACAGCUACAGCAGCAGCACUUU--CGGUUGUGGGGUCGCGCCAGCAAAAGGCUGCGAAGAGCGGCCGACAAUUGAAA
((((((........))))))..........................(((.(....).)))...((--(((((((.((.((((.(((((.....)))).)....)))))).))))))))). ( -31.30)
>DroSec_CAF1 24113 120 + 1
UUGACAAAUGGAAAUGUCAAAAUGAAAAAUUAACUGAAAAUCAACAGCUACAGCAGCAGCACUUUAUGGGGUGCGGGGUCGCGCCAGCAAAAGGCUGCGAAGAGCGGCCGACAAUUGAAA
((((((........))))))....................((((..(((...((.((.((((((....))))))...)).))...)))....((((((.....)))))).....)))).. ( -33.90)
>DroSim_CAF1 29063 120 + 1
UUGACAAAUGGAAAUGUCAAAAUGAAAAAUUAACUGAAAAUCAACAGCUACAGCAGCAGCACUUUAUGGGGUGCGGGGUCGCGCCAGCAAAAGGCUGCGAAGAGCGGCCGACAAUUGAAA
((((((........))))))....................((((..(((...((.((.((((((....))))))...)).))...)))....((((((.....)))))).....)))).. ( -33.90)
>DroEre_CAF1 23075 117 + 1
UUGACAAAUGGAAAUGUCAAAAUGAAAAAUUAACUGAAAAUCAACAGCUACGGCAGCAGCAGUU---CGGUUGAGAGGUCGCGCCAGUAAAAGGCUGCGAAGAGCGACCGACAAUUGAAA
((((((........)))))).........(((((((((........((....))........))---)))))))..((((((.(((((.....)))).)....))))))........... ( -32.69)
>DroYak_CAF1 25044 119 + 1
UUGACAAAUGGAAAUGUCAAAAUGAAAAAUUAACUGAAAAUCAACAGCUAACACGGCAGCAGUUCC-CGGUUGAGGGGUCGCGCCAGCAAAAGGCUGCGAAGAGCGACCGACAAUUGAAA
((((((........))))))..........................(((.....)))..(((((..-((((((.....(((((((.......))).))))....))))))..)))))... ( -29.60)
>consensus
UUGACAAAUGGAAAUGUCAAAAUGAAAAAUUAACUGAAAAUCAACAGCUACAGCAGCAGCACUUU__CGGUUGAGGGGUCGCGCCAGCAAAAGGCUGCGAAGAGCGGCCGACAAUUGAAA
((((((........))))))....................((((..(((.....))).(((((......)))))..((((((.(((((.....)))).)....)))))).....)))).. (-26.26 = -25.90 +  -0.36) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 1,398,309 – 1,398,427
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.31
Mean single sequence MFE -31.18
Consensus MFE -24.40
Energy contribution -24.40
Covariance contribution 0.00
Combinations/Pair 1.07
Mean z-score -2.41
Structure conservation index 0.78
SVM decision value 1.45
SVM RNA-class probability 0.955288
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1398309 118 - 20766785
UUUCAAUUGUCGGCCGCUCUUCGCAGCCUUUUGCUGGCGCGACCCCACAACCG--AAAGUGCUGCUGCUGUAGCUGUUGAUUUUCAGUUAAUUUUUCAUUUUGACAUUUCCAUUUGUCAA
........(((((((((.....))(((.....)))))).)))).....(((.(--((((((((((....))))).....)))))).)))...........((((((........)))))) ( -28.70)
>DroSec_CAF1 24113 120 - 1
UUUCAAUUGUCGGCCGCUCUUCGCAGCCUUUUGCUGGCGCGACCCCGCACCCCAUAAAGUGCUGCUGCUGUAGCUGUUGAUUUUCAGUUAAUUUUUCAUUUUGACAUUUCCAUUUGUCAA
....((((((((((.((((..((((((((((....((.(((....))).))....)))).))))).)..).))).)))))....)))))...........((((((........)))))) ( -32.60)
>DroSim_CAF1 29063 120 - 1
UUUCAAUUGUCGGCCGCUCUUCGCAGCCUUUUGCUGGCGCGACCCCGCACCCCAUAAAGUGCUGCUGCUGUAGCUGUUGAUUUUCAGUUAAUUUUUCAUUUUGACAUUUCCAUUUGUCAA
....((((((((((.((((..((((((((((....((.(((....))).))....)))).))))).)..).))).)))))....)))))...........((((((........)))))) ( -32.60)
>DroEre_CAF1 23075 117 - 1
UUUCAAUUGUCGGUCGCUCUUCGCAGCCUUUUACUGGCGCGACCUCUCAACCG---AACUGCUGCUGCCGUAGCUGUUGAUUUUCAGUUAAUUUUUCAUUUUGACAUUUCCAUUUGUCAA
..(((((..(((((......((((.(((.......))))))).......))))---)...(((((....))))).)))))....................((((((........)))))) ( -28.92)
>DroYak_CAF1 25044 119 - 1
UUUCAAUUGUCGGUCGCUCUUCGCAGCCUUUUGCUGGCGCGACCCCUCAACCG-GGAACUGCUGCCGUGUUAGCUGUUGAUUUUCAGUUAAUUUUUCAUUUUGACAUUUCCAUUUGUCAA
..........((((.((...((((.(((.......))))))).(((......)-))....)).)))).((((((((........))))))))........((((((........)))))) ( -33.10)
>consensus
UUUCAAUUGUCGGCCGCUCUUCGCAGCCUUUUGCUGGCGCGACCCCGCAACCG__AAAGUGCUGCUGCUGUAGCUGUUGAUUUUCAGUUAAUUUUUCAUUUUGACAUUUCCAUUUGUCAA
..........((((.((.((((((.(((.......)))))))...............)).)).))))...((((((........))))))..........((((((........)))))) (-24.40 = -24.40 +   0.00) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 1,398,349 – 1,398,466
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.02
Mean single sequence MFE -37.56
Consensus MFE -29.60
Energy contribution -29.28
Covariance contribution -0.32
Combinations/Pair 1.21
Mean z-score -1.53
Structure conservation index 0.79
SVM decision value 0.20
SVM RNA-class probability 0.629931
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1398349 117 + 20766785
UCAACAGCUACAGCAGCAGCACUUU--CGGUUGUGGGGUCGCGCCAGCAAAAGGCUGCGAAGAGCGGCCGACAAUUGAAAAUGUCAAAAUUCACGAGCCCAGUCAA-AGCGUGGAGAGGU
.......((((.((.(((((.....--..)))))(((.((((....))....((((((.....))))))((((........)))).........)).)))......-.))))))...... ( -35.80)
>DroSec_CAF1 24153 120 + 1
UCAACAGCUACAGCAGCAGCACUUUAUGGGGUGCGGGGUCGCGCCAGCAAAAGGCUGCGAAGAGCGGCCGACAAUUGAAAAUGUCAAAAUUCACGAGCCCAGCCAAAAGUGUGGAGAGGU
((..(.(((.....))).(((((((.(((((((((....)))))).((....((((((.....))))))((((........))))...........))....)))))))))))..))... ( -40.30)
>DroSim_CAF1 29103 120 + 1
UCAACAGCUACAGCAGCAGCACUUUAUGGGGUGCGGGGUCGCGCCAGCAAAAGGCUGCGAAGAGCGGCCGACAAUUGAAAAUGUCAAAAUUCACGAGCCCAGCCAAAAGUGUGGAGAGGU
((..(.(((.....))).(((((((.(((((((((....)))))).((....((((((.....))))))((((........))))...........))....)))))))))))..))... ( -40.30)
>DroEre_CAF1 23115 116 + 1
UCAACAGCUACGGCAGCAGCAGUU---CGGUUGAGAGGUCGCGCCAGUAAAAGGCUGCGAAGAGCGACCGACAAUUGAAAAUGUCAAAAUUCACGAGCCCAACCAA-AGCGUGGAUAGGU
......(((..((((....(((((---((((((.....(((((((.......))).))))....)))))))..))))....))))...(((((((...........-..))))))).))) ( -34.22)
>DroYak_CAF1 25084 115 + 1
UCAACAGCUAACACGGCAGCAGUUCC-CGGUUGAGGGGUCGCGCCAGCAAAAGGCUGCGAAGAGCGACCGACAAUUGAAAAUGUCAAAAUUCACGAGCUCAGCCAA-AGCUUGGU---GA
...........(((((((.(((((..-((((((.....(((((((.......))).))))....))))))..)))))....))))........((((((.......-))))))))---). ( -37.20)
>consensus
UCAACAGCUACAGCAGCAGCACUUU__CGGUUGAGGGGUCGCGCCAGCAAAAGGCUGCGAAGAGCGGCCGACAAUUGAAAAUGUCAAAAUUCACGAGCCCAGCCAA_AGCGUGGAGAGGU
.......((((.((....))........(((((.((((((((.(((((.....)))).)....))))))((((........))))............)))))))......))))...... (-29.60 = -29.28 +  -0.32) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 1,398,387 – 1,398,506
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.31
Mean single sequence MFE -31.46
Consensus MFE -21.27
Energy contribution -21.38
Covariance contribution 0.11
Combinations/Pair 1.14
Mean z-score -2.04
Structure conservation index 0.68
SVM decision value 0.17
SVM RNA-class probability 0.619249
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1398387 119 + 20766785
GCGCCAGCAAAAGGCUGCGAAGAGCGGCCGACAAUUGAAAAUGUCAAAAUUCACGAGCCCAGUCAA-AGCGUGGAGAGGUAACAGCCAUCCUCACAGCUAAACACUGUGAAAAAUUUUGU
......((((((((((((.....))))))((((........))))....(((((((......))..-((((((..(((((....))).))..))).))).......)))))...)))))) ( -34.50)
>DroSec_CAF1 24193 119 + 1
GCGCCAGCAAAAGGCUGCGAAGAGCGGCCGACAAUUGAAAAUGUCAAAAUUCACGAGCCCAGCCAAAAGUGUGGAGAGGUAACAGCCAUCCUCACGGCUAAACACUGUGAAAAAUU-GAU
((....))....((((((.....))))))((((........))))....((((((.....((((....(((.(((..(((....))).))).)))))))......)))))).....-... ( -36.70)
>DroSim_CAF1 29143 119 + 1
GCGCCAGCAAAAGGCUGCGAAGAGCGGCCGACAAUUGAAAAUGUCAAAAUUCACGAGCCCAGCCAAAAGUGUGGAGAGGUAACAGCCAUCCUCACAGCUAAACACUGUGAAAAAUU-GAU
((....))....((((((.....))))))((((........))))....((((((.....(((.....(((.(((..(((....))).))).))).)))......)))))).....-... ( -33.00)
>DroEre_CAF1 23152 117 + 1
GCGCCAGUAAAAGGCUGCGAAGAGCGACCGACAAUUGAAAAUGUCAAAAUUCACGAGCCCAACCAA-AGCGUGGAUAGGU-AAAGCCAUCCUAACGGCGGAACACUGCGAGAAAUG-AAU
.(((.(((....((((((.....)).(((((((........))))...(((((((...........-..))))))).)))-..)))).(((.......)))..)))))).......-... ( -28.12)
>DroYak_CAF1 25123 108 + 1
GCGCCAGCAAAAGGCUGCGAAGAGCGACCGACAAUUGAAAAUGUCAAAAUUCACGAGCUCAGCCAA-AGCUUGGU---GA-ACAGCC------ACAGCAAAACACUGUACAAAAUU-AAU
((....))....(((((............((((........))))....((((((((((.......-))))).))---))-))))))------((((.......))))........-... ( -25.00)
>consensus
GCGCCAGCAAAAGGCUGCGAAGAGCGGCCGACAAUUGAAAAUGUCAAAAUUCACGAGCCCAGCCAA_AGCGUGGAGAGGUAACAGCCAUCCUCACAGCUAAACACUGUGAAAAAUU_AAU
((.(((((....((((((.....))))))((((........)))).......................)).))).((((..........))))...))...................... (-21.27 = -21.38 +   0.11) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 1,398,387 – 1,398,506
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.31
Mean single sequence MFE -34.10
Consensus MFE -26.96
Energy contribution -28.96
Covariance contribution 2.00
Combinations/Pair 1.07
Mean z-score -1.72
Structure conservation index 0.79
SVM decision value 0.51
SVM RNA-class probability 0.762738
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1398387 119 - 20766785
ACAAAAUUUUUCACAGUGUUUAGCUGUGAGGAUGGCUGUUACCUCUCCACGCU-UUGACUGGGCUCGUGAAUUUUGACAUUUUCAAUUGUCGGCCGCUCUUCGCAGCCUUUUGCUGGCGC
.............(((((....(((((((((((((((..........((((((-(.....))))..)))......((((........))))))))).))))))))))....))))).... ( -36.60)
>DroSec_CAF1 24193 119 - 1
AUC-AAUUUUUCACAGUGUUUAGCCGUGAGGAUGGCUGUUACCUCUCCACACUUUUGGCUGGGCUCGUGAAUUUUGACAUUUUCAAUUGUCGGCCGCUCUUCGCAGCCUUUUGCUGGCGC
...-.....(((((.(.(((((((((.(((..(((..(......).)))..))).))))))))).))))))...(((((........)))))(((((.....))(((.....)))))).. ( -35.30)
>DroSim_CAF1 29143 119 - 1
AUC-AAUUUUUCACAGUGUUUAGCUGUGAGGAUGGCUGUUACCUCUCCACACUUUUGGCUGGGCUCGUGAAUUUUGACAUUUUCAAUUGUCGGCCGCUCUUCGCAGCCUUUUGCUGGCGC
...-.........(((((....(((((((((((((((....(((..(((......)))..)))............((((........))))))))).))))))))))....))))).... ( -37.40)
>DroEre_CAF1 23152 117 - 1
AUU-CAUUUCUCGCAGUGUUCCGCCGUUAGGAUGGCUUU-ACCUAUCCACGCU-UUGGUUGGGCUCGUGAAUUUUGACAUUUUCAAUUGUCGGUCGCUCUUCGCAGCCUUUUACUGGCGC
...-.................((((....((((((....-..)))))).....-..(((.(((((.(((((..((((((........))))))......))))))))))...))))))). ( -31.50)
>DroYak_CAF1 25123 108 - 1
AUU-AAUUUUGUACAGUGUUUUGCUGU------GGCUGU-UC---ACCAAGCU-UUGGCUGAGCUCGUGAAUUUUGACAUUUUCAAUUGUCGGUCGCUCUUCGCAGCCUUUUGCUGGCGC
...-......((.(((((....(((((------((..((-((---((((....-.))).)))))..((((....(((((........))))).))))...)))))))....))))))).. ( -29.70)
>consensus
AUC_AAUUUUUCACAGUGUUUAGCUGUGAGGAUGGCUGUUACCUCUCCACGCU_UUGGCUGGGCUCGUGAAUUUUGACAUUUUCAAUUGUCGGCCGCUCUUCGCAGCCUUUUGCUGGCGC
.............(((((....(((((((((((((((....(((..(((......)))..)))............((((........))))))))).))))))))))....))))).... (-26.96 = -28.96 +   2.00) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:29:01 2006