Locus 1205

Sequence ID 2R_DroMel_CAF1
Location 4,788,635 – 4,788,761
Length 126
Max. P 0.754651
window2094 window2095

overview

Window 4

Location 4,788,635 – 4,788,729
Length 94
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 69.77
Mean single sequence MFE -17.98
Consensus MFE -9.14
Energy contribution -11.45
Covariance contribution 2.31
Combinations/Pair 1.21
Mean z-score -1.79
Structure conservation index 0.51
SVM decision value 0.48
SVM RNA-class probability 0.754651
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4788635 94 + 20766785
CCAACAAAAAA-AAACAAGGAAAAGUGUCCAAAGCCAUAAGAAGGCGAUGUACUCUGUUGUACUCUAUGUACACUAGAUUUUAUCACAUUU-------UUCA
...........-.......(((((((((.....(((.......)))((((...((((.(((((.....))))).))))...))))))))))-------))). ( -24.40)
>DroSec_CAF1 11252 94 + 1
CCAAAAAAAAACAAAAAAGGAAAAGUGUCCAAAGCCAUAAGAAGGCGAAGUACUCUG-UGUACCCUAUGUACGCUAGAUUUUAUCACAUUU-------UACA
...................(.(((((((.....(((.......)))(((((.((..(-(((((.....)))))).)))))))...))))))-------).). ( -16.30)
>DroEre_CAF1 11473 84 + 1
GCAGAAAA-------AAAGGAAAAGUGUCCA-AGCCGAGAGACGGCUAUGUACUCUG----------UGUACCCUAGGCUUUAUCGCAUAUACGUAUGUAUA
(((((...-------...(((......))).-(((((.....)))))......))))----------)((((.....((......))......))))..... ( -17.50)
>DroYak_CAF1 11990 76 + 1
GCAGAAAA-------AAAGGAAAAGUGUCCA-AGCCAAGAAAAGGCGAUGUACUCUA----------CGUACCAUAGGUUUCAUCGCAUAU--------UUA
((......-------...(((......))).-.(((.......)))((((.((.(((----------.......)))))..))))))....--------... ( -13.70)
>consensus
CCAAAAAA_______AAAGGAAAAGUGUCCA_AGCCAAAAGAAGGCGAUGUACUCUG__________UGUACCCUAGAUUUUAUCACAUAU_______UACA
..................(((......)))...(((.......)))((((...((((.(((((.....))))).))))...))))................. ( -9.14 = -11.45 +   2.31)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,788,658 – 4,788,761
Length 103
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 68.44
Mean single sequence MFE -20.36
Consensus MFE -12.38
Energy contribution -14.58
Covariance contribution 2.20
Combinations/Pair 1.24
Mean z-score -1.42
Structure conservation index 0.61
SVM decision value 0.38
SVM RNA-class probability 0.714717
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4788658 103 + 20766785
GUGUCCAAAGCCAUAAGAAGGCGAUGUACUCUGUUGUACUCUAUGUACACUAGAUUUUAUCACAUUU-------UUCAAGACACAUUAAUAUUACCGCCGAGAUUCUUAA--------
(((((....(((.......)))((((...((((.(((((.....))))).))))...))))......-------.....)))))..........................-------- ( -23.00)
>DroSec_CAF1 11276 102 + 1
GUGUCCAAAGCCAUAAGAAGGCGAAGUACUCUG-UGUACCCUAUGUACGCUAGAUUUUAUCACAUUU-------UACAACACACAUUCGUACUACCGCUGAGAUUCUUAA--------
.............((((((((((.(((((...(-(((((.....))))))..(((...)))......-------..............)))))..))))....)))))).-------- ( -18.40)
>DroSim_CAF1 17982 105 + 1
GUGUCCAAAGCCAUAAGAAGGCGAAGUACUUUG-UGUACCCUAUGUACACUAGAUUUUAUCACAUUU-------UACAACACACAUUCGUAUUACGA-----AUUCCCACCACANNNN
((((.....(((.......)))(((((.((..(-(((((.....)))))).))))))).........-------....))))..(((((.....)))-----)).............. ( -19.30)
>DroEre_CAF1 11490 99 + 1
GUGUCCA-AGCCGAGAGACGGCUAUGUACUCUG----------UGUACCCUAGGCUUUAUCGCAUAUACGUAUGUAUAGGACACAUACAUUUUUUCAGUAACAUUCUUAA--------
((((((.-(((((.....))))).(((((..((----------((((......((......)).))))))...)))))))))))..........................-------- ( -25.00)
>DroYak_CAF1 12007 91 + 1
GUGUCCA-AGCCAAGAAAAGGCGAUGUACUCUA----------CGUACCAUAGGUUUCAUCGCAUAU--------UUAAGACACGUAGAUAUGACCAAUUAAAUUCUUAA--------
(((((..-.(((.......)))((((.((.(((----------.......)))))..))))......--------....)))))..........................-------- ( -16.10)
>consensus
GUGUCCAAAGCCAUAAGAAGGCGAUGUACUCUG_UGUAC_CUAUGUACACUAGAUUUUAUCACAUUU_______UACAAGACACAUUCAUAUUACCACUGAGAUUCUUAA________
(((((....(((.......)))((((...((((.(((((.....))))).))))...))))..................))))).................................. (-12.38 = -14.58 +   2.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:54 2006