Locus 5002

Sequence ID X_DroMel_CAF1
Location 13,079,458 – 13,079,705
Length 247
Max. P 0.999876
window8143 window8144 window8145 window8146 window8147 window8148

overview

Window 3

Location 13,079,458 – 13,079,575
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 77.39
Mean single sequence MFE -28.56
Consensus MFE -16.09
Energy contribution -15.53
Covariance contribution -0.56
Combinations/Pair 1.33
Mean z-score -2.58
Structure conservation index 0.56
SVM decision value 1.84
SVM RNA-class probability 0.979494
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13079458 117 + 22224390
GUGAGCAAAGUUAUUUCGAAUUGAGU-UUGCGUCAAGGUGAAGAUCAGCGCUGAGUAAGAUAGGUGCAAAUAUCUAGUAA--AAUUACUCAGCGCUGGAAUAAAACAUAUAUAUAUGUGC
.((((((((.(((........))).)-)))).))).........((((((((((((((..((((((....))))))....--..))))))))))))))......(((((....))))).. ( -37.60)
>DroSec_CAF1 28633 110 + 1
GUGAGUAAAGUUAUACAGAAUUGAGU-UUGCGUCAAGGUGAAGAUCAGCGCUGAGUAAGAUAUGUGCAAAUAUCUAGUAA--AAUUACUCAGCGUCGGAAUAAAACAUAUAUG-------
.((((((((.(((........))).)-)))).)))..((.....((.((((((((((((((((......)))))).....--...))))))))))..)).....)).......------- ( -26.70)
>DroEre_CAF1 28641 114 + 1
GCGAGUAAAGUUAUUCAGAAUUGCGA-UUGCGUCCAGAGGAUGAUCCGUGGUGAUUAAG-----AGCAAAUAUCUAGAAAAGAAUUAAUCAGCGCCGGAAUAAAACAUAUAUACUCGUAU
(((((((...................-...(((((...))))).((((((.(((((((.-----..(..............)..))))))).)).))))............))))))).. ( -25.54)
>DroYak_CAF1 31219 118 + 1
GUGAGUAAAGUUAUUCAGAAUUGAGUUUUGCAUCAAUGUGAAUAUCAUUGCCGAGUAAGCU-GGUGCAAAUAUCUAGCAAA-AAUUACUCAGCAGCAAAAUAAAACCUACAUAUAUAUGU
(((.((...(.((((((..(((((........))))).)))))).).((((.(((((((((-((.........)))))...-..)))))).)))).........)).))).......... ( -24.40)
>consensus
GUGAGUAAAGUUAUUCAGAAUUGAGU_UUGCGUCAAGGUGAAGAUCAGCGCUGAGUAAGAU_GGUGCAAAUAUCUAGUAA__AAUUACUCAGCGCCGGAAUAAAACAUAUAUAUAUGUGU
((((....((((......)))).....)))).............((.(((((((((((......(((.........))).....))))))))))).))...................... (-16.09 = -15.53 +  -0.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,079,458 – 13,079,575
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.39
Mean single sequence MFE -22.15
Consensus MFE -12.10
Energy contribution -12.22
Covariance contribution 0.12
Combinations/Pair 1.38
Mean z-score -2.12
Structure conservation index 0.55
SVM decision value 0.53
SVM RNA-class probability 0.771006
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13079458 117 - 22224390
GCACAUAUAUAUAUGUUUUAUUCCAGCGCUGAGUAAUU--UUACUAGAUAUUUGCACCUAUCUUACUCAGCGCUGAUCUUCACCUUGACGCAA-ACUCAAUUCGAAAUAACUUUGCUCAC
..(((((....))))).......((((((((((((...--.....(((((........)))))))))))))))))..........(((.((((-(................)))))))). ( -27.69)
>DroSec_CAF1 28633 110 - 1
-------CAUAUAUGUUUUAUUCCGACGCUGAGUAAUU--UUACUAGAUAUUUGCACAUAUCUUACUCAGCGCUGAUCUUCACCUUGACGCAA-ACUCAAUUCUGUAUAACUUUACUCAC
-------..(((((.......((.(.(((((((((...--.....((((((......)))))))))))))))).))........((((.....-..))))....)))))........... ( -18.30)
>DroEre_CAF1 28641 114 - 1
AUACGAGUAUAUAUGUUUUAUUCCGGCGCUGAUUAAUUCUUUUCUAGAUAUUUGCU-----CUUAAUCACCACGGAUCAUCCUCUGGACGCAA-UCGCAAUUCUGAAUAACUUUACUCGC
...((((((....(((((...(((((.(.(((((((.(((.....)))........-----.))))))).)..((.....)).))))).((..-..))......)))))....)))))). ( -19.10)
>DroYak_CAF1 31219 118 - 1
ACAUAUAUAUGUAGGUUUUAUUUUGCUGCUGAGUAAUU-UUUGCUAGAUAUUUGCACC-AGCUUACUCGGCAAUGAUAUUCACAUUGAUGCAAAACUCAAUUCUGAAUAACUUUACUCAC
.(((......(((((......)))))((((((((((((-..(((.........)))..-)).))))))))))))).((((((.(((((........)))))..))))))........... ( -23.50)
>consensus
ACACAUAUAUAUAUGUUUUAUUCCGGCGCUGAGUAAUU__UUACUAGAUAUUUGCACC_AUCUUACUCAGCACUGAUCUUCACCUUGACGCAA_ACUCAAUUCUGAAUAACUUUACUCAC
.......................(((((((((((((..........................)))))))))))))............................................. (-12.10 = -12.22 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 13,079,497 – 13,079,613
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 62.54
Mean single sequence MFE -24.51
Consensus MFE -14.62
Energy contribution -14.25
Covariance contribution -0.38
Combinations/Pair 1.44
Mean z-score -3.42
Structure conservation index 0.60
SVM decision value 4.34
SVM RNA-class probability 0.999876
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13079497 116 + 22224390
AAGAUCAGCGCUGAGUAAGAUAGGUGCAAAUAUCUAGUAA--AAUUACUCAGCGCUGGAAUAAAACAUAUAUAUAUGUGCAUACAUACA-AUAUAUGCAUAAAACGCAAAAAUCCCAAU-
....((((((((((((((..((((((....))))))....--..)))))))))))))).................((((((((......-...))))))))..................- ( -33.60)
>DroSec_CAF1 28672 91 + 1
AAGAUCAGCGCUGAGUAAGAUAUGUGCAAAUAUCUAGUAA--AAUUACUCAGCGUCGGAAUAAAACAUAUAUG--------------------------UAAACCACGGAAAUCCCAGU-
....((.((((((((((((((((......)))))).....--...)))))))))).))...............--------------------------........((.....))...- ( -21.00)
>DroEre_CAF1 28680 95 + 1
AUGAUCCGUGGUGAUUAAG-----AGCAAAUAUCUAGAAAAGAAUUAAUCAGCGCCGGAAUAAAACAUAUAUACUCGUAUCUACAUGAACGUAUAUGC------CA--------------
....((((((.(((((((.-----..(..............)..))))))).)).))))......(((((((..((((......))))..))))))).------..-------------- ( -19.04)
>DroYak_CAF1 31259 118 + 1
AAUAUCAUUGCCGAGUAAGCU-GGUGCAAAUAUCUAGCAAA-AAUUACUCAGCAGCAAAAUAAAACCUACAUAUAUAUGUAUAUACAGACAUAUAUGCAUAAGCCACAGAAAUCGCAGUG
.....((((((.(((((((((-((.........)))))...-..)))))).........................((((((((((......)))))))))).............)))))) ( -24.40)
>consensus
AAGAUCAGCGCUGAGUAAGAU_GGUGCAAAUAUCUAGUAA__AAUUACUCAGCGCCGGAAUAAAACAUAUAUAUAUGUGUAUACAUA_A_AUAUAUGC_UAAACCACAGAAAUCCCAGU_
....((.(((((((((((......(((.........))).....))))))))))).)).............................................................. (-14.62 = -14.25 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 13,079,497 – 13,079,613
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 62.54
Mean single sequence MFE -25.60
Consensus MFE -12.10
Energy contribution -12.22
Covariance contribution 0.12
Combinations/Pair 1.38
Mean z-score -2.63
Structure conservation index 0.47
SVM decision value 2.57
SVM RNA-class probability 0.995348
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13079497 116 - 22224390
-AUUGGGAUUUUUGCGUUUUAUGCAUAUAU-UGUAUGUAUGCACAUAUAUAUAUGUUUUAUUCCAGCGCUGAGUAAUU--UUACUAGAUAUUUGCACCUAUCUUACUCAGCGCUGAUCUU
-...(((((.............((((((((-.((((((....)))))))))))))).......((((((((((((...--.....(((((........)))))))))))))))))))))) ( -34.40)
>DroSec_CAF1 28672 91 - 1
-ACUGGGAUUUCCGUGGUUUA--------------------------CAUAUAUGUUUUAUUCCGACGCUGAGUAAUU--UUACUAGAUAUUUGCACAUAUCUUACUCAGCGCUGAUCUU
-...((((((..((..((..(--------------------------((....)))...))..)).(((((((((...--.....((((((......)))))))))))))))..)))))) ( -21.00)
>DroEre_CAF1 28680 95 - 1
--------------UG------GCAUAUACGUUCAUGUAGAUACGAGUAUAUAUGUUUUAUUCCGGCGCUGAUUAAUUCUUUUCUAGAUAUUUGCU-----CUUAAUCACCACGGAUCAU
--------------.(------(((((((..(((..........)))..))))))))....((((..(.(((((((.(((.....)))........-----.))))))).).)))).... ( -16.50)
>DroYak_CAF1 31259 118 - 1
CACUGCGAUUUCUGUGGCUUAUGCAUAUAUGUCUGUAUAUACAUAUAUAUGUAGGUUUUAUUUUGCUGCUGAGUAAUU-UUUGCUAGAUAUUUGCACC-AGCUUACUCGGCAAUGAUAUU
....((((.......(((((((..((((((((........))))))))..))))))).....))))((((((((((((-..(((.........)))..-)).))))))))))........ ( -30.50)
>consensus
_ACUGGGAUUUCUGUGGUUUA_GCAUAUAU_U_UAUGUAUACACAUAUAUAUAUGUUUUAUUCCGGCGCUGAGUAAUU__UUACUAGAUAUUUGCACC_AUCUUACUCAGCACUGAUCUU
...............................................................(((((((((((((..........................)))))))))))))..... (-12.10 = -12.22 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 13,079,613 – 13,079,705
Length 92
Sequences 3
Columns 99
Reading direction forward
Mean pairwise identity 87.93
Mean single sequence MFE -35.93
Consensus MFE -30.43
Energy contribution -30.77
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.23
Structure conservation index 0.85
SVM decision value 1.61
SVM RNA-class probability 0.967500
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13079613 92 + 22224390
-------GAGUUGAAGUGCUGGAAGCAAAUGGAAGAGGUUUUUCUGGUCUCCAGUUGCCCGACACUCACAGCUCCCCAGCACUUUAGCUCCACGAUUUC
-------(((((((((((((((.(((........(.(((....((((...))))..))))(.....)...)))..)))))))))))))))......... ( -34.40)
>DroSec_CAF1 28763 92 + 1
-------GAGUUGAAGUGCUGGAAGCAAAUGGAAGAGGUUUUUCUGGUCUCCAGUUGCCCGACACUUUUAGCUCCGCAGCACUUUAGCUCCACGAUUUC
-------(((((((((((((((.((((((..(..(.(((....((((...))))..))))..)...))).))).).))))))))))))))......... ( -33.40)
>DroYak_CAF1 31377 99 + 1
AGUGAGUGAGUUGAAGUGCUGGGAGCAAAUCGAAGAGGUUUUUCUGGUCCCCAGUUGCCCGACACUCGUAGCUCCCCAGCACUUAAGCUCCCCGCUUUC
((((.(.(((((.(((((((((((((....(((.(.(((....((((...))))..)))).....)))..))).)))))))))).)))))).))))... ( -40.00)
>consensus
_______GAGUUGAAGUGCUGGAAGCAAAUGGAAGAGGUUUUUCUGGUCUCCAGUUGCCCGACACUCAUAGCUCCCCAGCACUUUAGCUCCACGAUUUC
.......(((((((((((((((.(((.....(..(.(((....((((...))))..))))..).......))).).))))))))))))))......... (-30.43 = -30.77 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 13,079,613 – 13,079,705
Length 92
Sequences 3
Columns 99
Reading direction reverse
Mean pairwise identity 87.93
Mean single sequence MFE -30.20
Consensus MFE -27.57
Energy contribution -27.13
Covariance contribution -0.44
Combinations/Pair 1.09
Mean z-score -1.52
Structure conservation index 0.91
SVM decision value 0.33
SVM RNA-class probability 0.690998
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13079613 92 - 22224390
GAAAUCGUGGAGCUAAAGUGCUGGGGAGCUGUGAGUGUCGGGCAACUGGAGACCAGAAAAACCUCUUCCAUUUGCUUCCAGCACUUCAACUC-------
.........(((...((((((((((.(((.(((.....(((....)))(((...........)))...)))..)))))))))))))...)))------- ( -27.60)
>DroSec_CAF1 28763 92 - 1
GAAAUCGUGGAGCUAAAGUGCUGCGGAGCUAAAAGUGUCGGGCAACUGGAGACCAGAAAAACCUCUUCCAUUUGCUUCCAGCACUUCAACUC-------
.........(((...((((((((.(((((...(((((.(((....)))(((...........)))...))))))))))))))))))...)))------- ( -26.90)
>DroYak_CAF1 31377 99 - 1
GAAAGCGGGGAGCUUAAGUGCUGGGGAGCUACGAGUGUCGGGCAACUGGGGACCAGAAAAACCUCUUCGAUUUGCUCCCAGCACUUCAACUCACUCACU
...((.((((((...((((((((((.(((..((((....((....))((((..........))))))))....)))))))))))))...))).))).)) ( -36.10)
>consensus
GAAAUCGUGGAGCUAAAGUGCUGGGGAGCUAAGAGUGUCGGGCAACUGGAGACCAGAAAAACCUCUUCCAUUUGCUUCCAGCACUUCAACUC_______
.........(((...((((((((.(((((.........(((....)))(((...........)))........)))))))))))))...)))....... (-27.57 = -27.13 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:37:54 2006