Locus 973

Sequence ID 3L_DroMel_CAF1
Location 2,898,260 – 2,898,393
Length 133
Max. P 0.997518
window1498 window1499 window1500

overview

Window 8

Location 2,898,260 – 2,898,354
Length 94
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.91
Mean single sequence MFE -32.65
Consensus MFE -16.67
Energy contribution -19.00
Covariance contribution 2.33
Combinations/Pair 1.00
Mean z-score -3.31
Structure conservation index 0.51
SVM decision value 2.84
SVM RNA-class probability 0.997362
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2898260 94 + 23771897
UGAUUUGCAUGCAAAUAAGCCAGAUUUU-----------CCA---AUCCCGCCUC--AUCCGAAGGACUC-AUGUCCUUCACAUGCUAGGUGGAACUGCCA---------GAUUUGGCAA
..(((((....)))))..(((((((((.-----------.((---...(((((((--((..(((((((..-..)))))))..)))..))))))...))..)---------)))))))).. ( -35.30)
>DroSec_CAF1 142675 94 + 1
UGAUUUGCAUGCAAAUAAGCCAGAUUUU-----------CCA---AUCCCGCCUC--AUCCGAAGGACUC-AUGUCCUUCACAUGCUAGGUGGAACUGCCA---------GAUUUGGCAA
..(((((....)))))..(((((((((.-----------.((---...(((((((--((..(((((((..-..)))))))..)))..))))))...))..)---------)))))))).. ( -35.30)
>DroSim_CAF1 133844 94 + 1
UGAUUUGCAUGCAAAUAAGCCAGAUUUU-----------CCA---AUCCCGCCGC--AUCCGAAGGACUC-AUGUCCUUCACAUGCUAGGUGGAACUGCCA---------GAUUUGGCAA
..(((((....)))))..(((((((((.-----------.((---...(((((((--((..(((((((..-..)))))))..))))..)))))...))..)---------)))))))).. ( -37.10)
>DroEre_CAF1 149935 98 + 1
UGAUUUGCAUGCAAAUAAGCCAGAUUUU-----------CCUCAUUUUCCGCCUC--AUCCGAAGGACGAAAUAUCCUCCACAUGCUAGGUGGCACUGCCA---------GAUUUGGCAA
..(((((....)))))..(((((((((.-----------...((....(((((((--((..(.((((.......)))).)..)))..))))))...))..)---------)))))))).. ( -24.00)
>DroYak_CAF1 151128 94 + 1
UGAUUUGCAUGCAAAUAAGCCAGAUUUU-----------CCA---AUACCGACAC--AACCGAAGGACGA-AUAUCCUUCACAUGCGUGGUGGCACUGCCA---------GAUUUGGCAA
..(((((....)))))..(((((((((.-----------...---..(((.((.(--(...((((((...-...))))))...)).)))))(((...))))---------)))))))).. ( -28.00)
>DroAna_CAF1 131172 114 + 1
UGAUUUGCAUGCAAAUAGGCCAGCCAGCCAGACAGGCAGCCA---GGCAGGACUCGGAUCC--AGGACGC-AGGCCAUAACCCUGCCAAAUGCAGAUCCCGCAUUGUUUGGCUUUGACCC
..(((((....))))).((.(((..((((((((((((((((.---....)).)).((((((--(....((-(((.......)))))....))..))))).)).))))))))))))).)). ( -36.20)
>consensus
UGAUUUGCAUGCAAAUAAGCCAGAUUUU___________CCA___AUCCCGCCUC__AUCCGAAGGACGC_AUGUCCUUCACAUGCUAGGUGGAACUGCCA_________GAUUUGGCAA
..(((((....)))))..((((((((...................................(((((((.....)))))))........(((......)))..........)))))))).. (-16.67 = -19.00 +   2.33)

alignment

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secondary structure

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dotplot

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Window 9

Location 2,898,260 – 2,898,354
Length 94
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.91
Mean single sequence MFE -37.17
Consensus MFE -19.90
Energy contribution -20.88
Covariance contribution 0.98
Combinations/Pair 1.31
Mean z-score -3.35
Structure conservation index 0.54
SVM decision value 2.87
SVM RNA-class probability 0.997518
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2898260 94 - 23771897
UUGCCAAAUC---------UGGCAGUUCCACCUAGCAUGUGAAGGACAU-GAGUCCUUCGGAU--GAGGCGGGAU---UGG-----------AAAAUCUGGCUUAUUUGCAUGCAAAUCA
((((((....---------)))))).........(((((((((((((..-..)))))))((((--(((.(.((((---(..-----------..))))).))))))))))))))...... ( -38.50)
>DroSec_CAF1 142675 94 - 1
UUGCCAAAUC---------UGGCAGUUCCACCUAGCAUGUGAAGGACAU-GAGUCCUUCGGAU--GAGGCGGGAU---UGG-----------AAAAUCUGGCUUAUUUGCAUGCAAAUCA
((((((....---------)))))).........(((((((((((((..-..)))))))((((--(((.(.((((---(..-----------..))))).))))))))))))))...... ( -38.50)
>DroSim_CAF1 133844 94 - 1
UUGCCAAAUC---------UGGCAGUUCCACCUAGCAUGUGAAGGACAU-GAGUCCUUCGGAU--GCGGCGGGAU---UGG-----------AAAAUCUGGCUUAUUUGCAUGCAAAUCA
((((((....---------)))))).........((((.((((((((..-..)))))))).))--))(((.((((---(..-----------..))))).))).(((((....))))).. ( -37.80)
>DroEre_CAF1 149935 98 - 1
UUGCCAAAUC---------UGGCAGUGCCACCUAGCAUGUGGAGGAUAUUUCGUCCUUCGGAU--GAGGCGGAAAAUGAGG-----------AAAAUCUGGCUUAUUUGCAUGCAAAUCA
((((((....---------)))))).........(((((((((((((.....)))))))((((--(((.((((........-----------....)))).)))))))))))))...... ( -33.20)
>DroYak_CAF1 151128 94 - 1
UUGCCAAAUC---------UGGCAGUGCCACCACGCAUGUGAAGGAUAU-UCGUCCUUCGGUU--GUGUCGGUAU---UGG-----------AAAAUCUGGCUUAUUUGCAUGCAAAUCA
.(((((....---------)))))(((....)))(((((((((((((..-..)))))))....--..(((((.((---(..-----------..))))))))......))))))...... ( -32.10)
>DroAna_CAF1 131172 114 - 1
GGGUCAAAGCCAAACAAUGCGGGAUCUGCAUUUGGCAGGGUUAUGGCCU-GCGUCCU--GGAUCCGAGUCCUGCC---UGGCUGCCUGUCUGGCUGGCUGGCCUAUUUGCAUGCAAAUCA
((((((..((((..((..(((((....((....((((((..(.(((((.-.......--))..))))..))))))---..))..))))).))..))))))))))(((((....))))).. ( -42.90)
>consensus
UUGCCAAAUC_________UGGCAGUUCCACCUAGCAUGUGAAGGACAU_GAGUCCUUCGGAU__GAGGCGGGAU___UGG___________AAAAUCUGGCUUAUUUGCAUGCAAAUCA
(((((...............))))).........(((((((((((((.....))))))).......((((.((((....................)))).))))....))))))...... (-19.90 = -20.88 +   0.98)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,898,289 – 2,898,393
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.66
Mean single sequence MFE -38.37
Consensus MFE -20.34
Energy contribution -20.68
Covariance contribution 0.34
Combinations/Pair 1.37
Mean z-score -1.80
Structure conservation index 0.53
SVM decision value 0.00
SVM RNA-class probability 0.534068
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2898289 104 - 23771897
-GCGACGAAGCGAUUAACCGUGUCAUUCCCGCAUAUUUGUUUGCCAAAUC---------UGGCAGUUCCACCUAGCAUGUGAAGGACAU-GAGUCCUUCGGAU--GAGGCGGGAU---UG
-..(((...(((......))))))..((((((........((((((....---------))))))..........(((.((((((((..-..)))))))).))--)..)))))).---.. ( -38.30)
>DroSec_CAF1 142704 104 - 1
-GCGACGAAGCGAUGAACCGUGACAUUCCCGCAUAUUUGCUUGCCAAAUC---------UGGCAGUUCCACCUAGCAUGUGAAGGACAU-GAGUCCUUCGGAU--GAGGCGGGAU---UG
-((......))............((.((((((........((((((....---------))))))..........(((.((((((((..-..)))))))).))--)..)))))).---)) ( -37.30)
>DroSim_CAF1 133873 104 - 1
-GCGACGAAGCGAUGAACCGUGACAUUCCCGCAUAUUUGCUUGCCAAAUC---------UGGCAGUUCCACCUAGCAUGUGAAGGACAU-GAGUCCUUCGGAU--GCGGCGGGAU---UG
-((......))............((.((((((........((((((....---------)))))).........((((.((((((((..-..)))))))).))--)).)))))).---)) ( -41.30)
>DroEre_CAF1 149964 108 - 1
-GCGACGAAGCGAUGAGCCGUGACAUUCCCGCAUAUUUGUUUGCCAAAUC---------UGGCAGUGCCACCUAGCAUGUGGAGGAUAUUUCGUCCUUCGGAU--GAGGCGGAAAAUGAG
-((......))......((((..(((((((((((......((((((....---------)))))).((......))))))))(((((.....)))))..))))--)..))))........ ( -31.40)
>DroYak_CAF1 151157 104 - 1
-GCGACGAAGCGAUGAACCGUGACACUCCCGCAUAUUUGUUUGCCAAAUC---------UGGCAGUGCCACCACGCAUGUGAAGGAUAU-UCGUCCUUCGGUU--GUGUCGGUAU---UG
-((......)).....(((..(((((..((((.........(((((....---------)))))(((....)))))....(((((((..-..)))))))))..--))))))))..---.. ( -33.90)
>DroAna_CAF1 131212 114 - 1
GGCAGCGAAGCGUUGAACCAUGACAUGCCAGCAUAUUUGCGGGUCAAAGCCAAACAAUGCGGGAUCUGCAUUUGGCAGGGUUAUGGCCU-GCGUCCU--GGAUCCGAGUCCUGCC---UG
(((((.((..((..((.(((.((((((....)))....((((((((.((((...((((((((...))))).)))....)))).))))))-))))).)--)).))))..)))))))---.. ( -48.00)
>consensus
_GCGACGAAGCGAUGAACCGUGACAUUCCCGCAUAUUUGCUUGCCAAAUC_________UGGCAGUUCCACCUAGCAUGUGAAGGACAU_GAGUCCUUCGGAU__GAGGCGGGAU___UG
.((......))...................(((....)))(((((...............)))))((((.(((...((.((((((((.....)))))))).))...))).))))...... (-20.34 = -20.68 +   0.34)

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 09:55:47 2006