Locus 550

Sequence ID X_DroMel_CAF1
Location 1,581,740 – 1,581,877
Length 137
Max. P 0.999544
window864 window865 window866

overview

Window 4

Location 1,581,740 – 1,581,840
Length 100
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 69.21
Mean single sequence MFE -37.94
Consensus MFE -14.90
Energy contribution -17.74
Covariance contribution 2.84
Combinations/Pair 1.05
Mean z-score -3.05
Structure conservation index 0.39
SVM decision value 3.71
SVM RNA-class probability 0.999544
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1581740 100 + 22224390
UGCCG--UAGC----AGCAU----AAUGUCGCAUUCAUUAAGCCAAACAGCAGGUGAUGCACACCUGCGGCUCC--AGCUGC-CUAGCUGCC-UAGCUGCCUGGCUCCCUGCUC
.((((--..((----(((.(----((((.......)))))((((.....(((((((.....))))))))))).(--((((..-..)))))..-..))))).))))......... ( -35.90)
>DroSec_CAF1 43269 92 + 1
UGCCA--UAGC----AGCAU----AAUGUCGCAUUCAUUAAGCCAAACAGCAGGUGAUGCACACCUGCGGCUCC--AGCUGC-CU---------AGCUGCCUGGCUCCCUGCUU
.....--.(((----((..(----((((.......)))))(((((..(((((((((.....)))))(((((...--.)))))-..---------.))))..)))))..))))). ( -34.10)
>DroEre_CAF1 46505 102 + 1
UGCCGCACAGC----AGCAU----AAUGUCGCAUUCAUUAAGCCAAACAGCAGGUGAUGCACACCUGCGGCUCC--AGCUGU-GUGGCUGCC-UGGCUGCCUGGCUGCCAGGUC
.((((((((((----....(----((((.......)))))((((.....(((((((.....)))))))))))..--.)))))-))))).(((-((((.((...)).))))))). ( -51.80)
>DroMoj_CAF1 53938 101 + 1
UGCUCAGUUGUGGCAUGCAUACGGAUUGUCGCAUUCAUUAGGGAAAACAGCAGGUGAUACGCACCUGGUGCGCCGCAGAUGCUCUAGCUGCCAUAGCUGCC-------------
....(((((((((((.((.((.((.((((.((.(((......)))..((.((((((.....)))))).)).)).))))...)).)))))))))))))))..------------- ( -36.80)
>DroAna_CAF1 58022 82 + 1
-GCCU--GGGU----G--GU----AAUGUCGCAUUCAUUAAGCCAAACAGCAGGUGAUGCACACCUGCGGCUCC--AGGUGC-UUCUCCUCC-CAGCUA---------------
-((.(--(((.----(--(.----...(..(((((.....((((.....(((((((.....)))))))))))..--.)))))-..).)).))-))))..--------------- ( -31.10)
>consensus
UGCCG__UAGC____AGCAU____AAUGUCGCAUUCAUUAAGCCAAACAGCAGGUGAUGCACACCUGCGGCUCC__AGCUGC_CUAGCUGCC_UAGCUGCCUGGCU_CC_G_U_
........................................(((((..(((((((((.....)))))(((((......))))).............))))..)))))........ (-14.90 = -17.74 +   2.84)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,581,740 – 1,581,840
Length 100
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 69.21
Mean single sequence MFE -38.50
Consensus MFE -18.42
Energy contribution -19.18
Covariance contribution 0.76
Combinations/Pair 1.15
Mean z-score -2.45
Structure conservation index 0.48
SVM decision value 2.65
SVM RNA-class probability 0.996077
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1581740 100 - 22224390
GAGCAGGGAGCCAGGCAGCUA-GGCAGCUAG-GCAGCU--GGAGCCGCAGGUGUGCAUCACCUGCUGUUUGGCUUAAUGAAUGCGACAUU----AUGCU----GCUA--CGGCA
.((((..(((((((((((((.-..(((((..-..))))--).))).(((((((.....)))))))))))))))))((((.......))))----.))))----((..--..)). ( -43.20)
>DroSec_CAF1 43269 92 - 1
AAGCAGGGAGCCAGGCAGCU---------AG-GCAGCU--GGAGCCGCAGGUGUGCAUCACCUGCUGUUUGGCUUAAUGAAUGCGACAUU----AUGCU----GCUA--UGGCA
.(((((.((((((((((...---------.(-((....--...)))(((((((.....)))))))))))))))))((((.......))))----...))----))).--..... ( -37.90)
>DroEre_CAF1 46505 102 - 1
GACCUGGCAGCCAGGCAGCCA-GGCAGCCAC-ACAGCU--GGAGCCGCAGGUGUGCAUCACCUGCUGUUUGGCUUAAUGAAUGCGACAUU----AUGCU----GCUGUGCGGCA
(.((((((.((...)).))))-))).(((.(-(((((.--.((((.(((((((.....))))))).))))(((.(((((.......))))----).)))----)))))).))). ( -50.70)
>DroMoj_CAF1 53938 101 - 1
-------------GGCAGCUAUGGCAGCUAGAGCAUCUGCGGCGCACCAGGUGCGUAUCACCUGCUGUUUUCCCUAAUGAAUGCGACAAUCCGUAUGCAUGCCACAACUGAGCA
-------------((((((.(((((((.....(((((((.(.....)))))))).......)))))))............(((((......))))))).))))........... ( -29.30)
>DroAna_CAF1 58022 82 - 1
---------------UAGCUG-GGAGGAGAA-GCACCU--GGAGCCGCAGGUGUGCAUCACCUGCUGUUUGGCUUAAUGAAUGCGACAUU----AC--C----ACCC--AGGC-
---------------...(((-((.((.((.-(((...--.((((((((((((.....))))))).....)))))......)))....))----.)--)----.)))--))..- ( -31.40)
>consensus
_A_C_GG_AGCCAGGCAGCUA_GGCAGCUAG_GCAGCU__GGAGCCGCAGGUGUGCAUCACCUGCUGUUUGGCUUAAUGAAUGCGACAUU____AUGCU____GCUA__CGGCA
.................(((............(((......((((((((((((.....))))))).....)))))......)))............((.....)).....))). (-18.42 = -19.18 +   0.76)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,581,764 – 1,581,877
Length 113
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 69.26
Mean single sequence MFE -37.49
Consensus MFE -23.33
Energy contribution -24.70
Covariance contribution 1.37
Combinations/Pair 1.13
Mean z-score -1.53
Structure conservation index 0.62
SVM decision value 0.88
SVM RNA-class probability 0.874193
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1581764 113 + 22224390
UCAUUAAGCCAAACAGCAGGUGAUGCACACCUGCGGCUCCAGCUGCCUAGCUGCCUAGCUGCCUGGCUCCCUGCUC---UGAGCUGCGAGCUGCGAGCUCCAGGUUUCGUCCUCCG
.....(((((.....(((((((.....)))))))((((((((((((.(((((....)))))...(((((.......---.))))))).))))).)))))...)))))......... ( -42.90)
>DroSec_CAF1 43293 105 + 1
UCAUUAAGCCAAACAGCAGGUGAUGCACACCUGCGGCUCCAGCUGCCU--------AGCUGCCUGGCUCCCUGCUU---UGAGCUGCGAGCUUCGAGCUCCAGGUUUCGUCCUCCG
......(((((..(((((((((.....)))))(((((....)))))..--------.))))..))))).((((...---.(((((.((.....)))))))))))............ ( -39.20)
>DroEre_CAF1 46531 116 + 1
UCAUUAAGCCAAACAGCAGGUGAUGCACACCUGCGGCUCCAGCUGUGUGGCUGCCUGGCUGCCUGGCUGCCAGGUCCUCCCUGCGCCGAGUUCCGAGCUCUAGGUCUCAUCCUGCG
......(((((.((.(((((((.....)))))))(((....))))).)))))(((((((.((...)).))))))).......((...((((.....)))).(((......))))). ( -45.10)
>DroAna_CAF1 58043 92 + 1
UCAUUAAGCCAAACAGCAGGUGAUGCACACCUGCGGCUCCAGGUGCUUCUCCUCCCAGCUA---------------CUCCC----CUGUGUUCUGUACUCUG-----UACUCUGCA
......((((.....(((((((.....))))))))))).(((((((.........(((.((---------------(....----..)))..)))......)-----))).))).. ( -22.76)
>consensus
UCAUUAAGCCAAACAGCAGGUGAUGCACACCUGCGGCUCCAGCUGCCU_GCUGCCUAGCUGCCUGGCUCCCUGCUC___CCAGCUCCGAGCUCCGAGCUCCAGGUUUCAUCCUCCG
......(((((..(((((((((.....)))))(((((....)))))...........))))..)))))...................((((.....))))................ (-23.33 = -24.70 +   1.37)

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 09:47:30 2006