Locus 1883

Sequence ID X_DroMel_CAF1
Location 5,220,662 – 5,220,790
Length 128
Max. P 0.981818
window3056 window3057 window3058

overview

Window 6

Location 5,220,662 – 5,220,759
Length 97
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 71.80
Mean single sequence MFE -18.62
Consensus MFE -5.83
Energy contribution -6.74
Covariance contribution 0.91
Combinations/Pair 1.33
Mean z-score -2.73
Structure conservation index 0.31
SVM decision value 1.90
SVM RNA-class probability 0.981818
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5220662 97 + 22224390
U-UC-UU-UUUAUUUCCCAUCCGCCCUUUUGAAAUCCGGG-UAUCAUCUCGUG----CUUUUU----UCGUCUAAUUUUGGUUAGACGAAAAUAAUUGGAUUUACACCG-
.-..-..-.....................(((((((((((-(((......)))----)))(((----(((((((((....)))))))))))).....)))))).))...- ( -21.80)
>DroPse_CAF1 45637 93 + 1
U-UUGCU-GUUAUUUUCUGU-UUCGUUUAC-CAUUU-------UUGUUCCUUGAAUUUUUUUU----UCGC--UGUUUUGGUUAGACCAAAAUAAUUGGAUUUACACCCA
.-.....-............-........(-((...-------.........(((.......)----))..--((((((((.....))))))))..)))........... ( -10.10)
>DroSec_CAF1 40487 95 + 1
U-UC-UU-UU--UUUCCCAUCCGCCCUUUC-AAAUCCGGGCUAUCAUCUCGUG----UUUUUU----UCGUCUAAUUUUGGUUAGACGAAAAUAAUUGGAUGUACACCG-
.-..-..-..--.....(((((((((....-......))))...........(----((.(((----(((((((((....)))))))))))).))).))))).......- ( -26.70)
>DroEre_CAF1 44025 97 + 1
UUUC-UU-UUUAUUUCCCAACCGCCCUUUC-AAAUCCGGGCU-ACAUCCCGUG----CUUUUU----UCGUCUAAUUUUGGUUAGACGAAAAUAAUUGGAUUUACACCG-
....-..-..............((((....-......)))).-..((((.((.----...(((----(((((((((....))))))))))))..)).))))........- ( -23.60)
>DroYak_CAF1 41311 83 + 1
U-UC-UU-UUUAUUUCCCGUCCGCUCUUUC-AAAUCCGG------------------CUUUUU----UCGUCUAAUUUUGGUUAGACGAAAAUAAUUGGAUUUACACCG-
.-..-..-......................-((((((((------------------...(((----(((((((((....))))))))))))...))))))))......- ( -21.10)
>DroAna_CAF1 47164 93 + 1
U-UC-CUCCUUUAUUCCGAGCUGCCCUUUC-AAUUCCAC--UUCCA-----------CUUUUUAUCCUUUUCUAUUUUUGGUUGGACAAAAAUAAUUGGAUUUACACCG-
.-..-.........................-........--.....-----------......((((.....((((((((......))))))))...))))........- (  -8.40)
>consensus
U_UC_UU_UUUAUUUCCCAUCCGCCCUUUC_AAAUCCGG__U_UCAUC_CGUG____CUUUUU____UCGUCUAAUUUUGGUUAGACGAAAAUAAUUGGAUUUACACCG_
..............(((...(((.............)))............................(((((((((....)))))))))........))).......... ( -5.83 =  -6.74 +   0.91)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,220,662 – 5,220,759
Length 97
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 71.80
Mean single sequence MFE -19.36
Consensus MFE -4.84
Energy contribution -6.30
Covariance contribution 1.46
Combinations/Pair 1.21
Mean z-score -2.42
Structure conservation index 0.25
SVM decision value 0.63
SVM RNA-class probability 0.806444
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5220662 97 - 22224390
-CGGUGUAAAUCCAAUUAUUUUCGUCUAACCAAAAUUAGACGA----AAAAAG----CACGAGAUGAUA-CCCGGAUUUCAAAAGGGCGGAUGGGAAAUAAA-AA-GA-A
-........((((.....(((((((((((......))))))))----)))...----............-(((...........))).))))..........-..-..-. ( -19.50)
>DroPse_CAF1 45637 93 - 1
UGGGUGUAAAUCCAAUUAUUUUGGUCUAACCAAAACA--GCGA----AAAAAAAAUUCAAGGAACAA-------AAAUG-GUAAACGAA-ACAGAAAAUAAC-AGCAA-A
(((((....)))))....((((((.....))))))..--((((----(.......))).........-------...((-.....))..-............-.))..-. ( -10.20)
>DroSec_CAF1 40487 95 - 1
-CGGUGUACAUCCAAUUAUUUUCGUCUAACCAAAAUUAGACGA----AAAAAA----CACGAGAUGAUAGCCCGGAUUU-GAAAGGGCGGAUGGGAAA--AA-AA-GA-A
-.......(((((.....(((((((((((......))))))))----)))...----............((((......-....))))))))).....--..-..-..-. ( -27.40)
>DroEre_CAF1 44025 97 - 1
-CGGUGUAAAUCCAAUUAUUUUCGUCUAACCAAAAUUAGACGA----AAAAAG----CACGGGAUGU-AGCCCGGAUUU-GAAAGGGCGGUUGGGAAAUAAA-AA-GAAA
-.........(((((((.(((((((((((......))))))))----)))...----..........-.((((......-....))))))))))).......-..-.... ( -25.50)
>DroYak_CAF1 41311 83 - 1
-CGGUGUAAAUCCAAUUAUUUUCGUCUAACCAAAAUUAGACGA----AAAAAG------------------CCGGAUUU-GAAAGAGCGGACGGGAAAUAAA-AA-GA-A
-(.((.(((((((..((.(((((((((((......))))))))----))).))------------------..))))))-).....)).)............-..-..-. ( -19.30)
>DroAna_CAF1 47164 93 - 1
-CGGUGUAAAUCCAAUUAUUUUUGUCCAACCAAAAAUAGAAAAGGAUAAAAAG-----------UGGAA--GUGGAAUU-GAAAGGGCAGCUCGGAAUAAAGGAG-GA-A
-((((.((..((((....(((((((((................))))))))).-----------)))).--.))..)))-).........(((.........)))-..-. ( -14.29)
>consensus
_CGGUGUAAAUCCAAUUAUUUUCGUCUAACCAAAAUUAGACGA____AAAAAG____CACG_GAUGA_A__CCGGAUUU_GAAAGGGCGGAUGGGAAAUAAA_AA_GA_A
..........(((........((((((((......))))))))............................(((.............)))...))).............. ( -4.84 =  -6.30 +   1.46)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,220,689 – 5,220,790
Length 101
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 73.49
Mean single sequence MFE -23.05
Consensus MFE -10.31
Energy contribution -11.48
Covariance contribution 1.17
Combinations/Pair 1.14
Mean z-score -2.03
Structure conservation index 0.45
SVM decision value 0.79
SVM RNA-class probability 0.850683
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5220689 101 - 22224390
--------CUUUGCCUGGUUUCCAUCUAGAUUCUUGAUU--CGGUGUAAAUCCAAUUAUUUUCGUCUAACCAAAAUUAGACGAAAAAAG----CACGAGAUGAUA-CCCGGAUUUC
--------.....((.(((...(((((.......(((((--.(((....))).)))))(((((((((((......)))))))))))...----....)))))..)-)).))..... ( -25.00)
>DroPse_CAF1 45664 105 - 1
UGUGUGGACUUUCUCUGGUUU-CAUCUUGAUUCUUGGUUUUGGGUGUAAAUCCAAUUAUUUUGGUCUAACCAAAACA--GCGAAAAAAAAAUUCAAGGAACAA-------AAAUG-
.(((.(((((......)))))-))).(((.(((((((..((((((....))))))...((((((.....))))))..--.............))))))).)))-------.....- ( -19.90)
>DroSec_CAF1 40512 101 - 1
--------CUUUGCCUGGUUUCCAUCUAGAUUCUUGAUU--CGGUGUACAUCCAAUUAUUUUCGUCUAACCAAAAUUAGACGAAAAAAA----CACGAGAUGAUAGCCCGGAUUU-
--------.....((.((((..(((((.......(((((--.(((....))).)))))(((((((((((......)))))))))))...----....)))))..)))).))....- ( -27.00)
>DroEre_CAF1 44053 100 - 1
--------CUUUCCCUGGCCUCCAUCUAGACUCUUGAUU--CGGUGUAAAUCCAAUUAUUUUCGUCUAACCAAAAUUAGACGAAAAAAG----CACGGGAUGU-AGCCCGGAUUU-
--------......((((.((.(((((.......(((((--.(((....))).)))))(((((((((((......)))))))))))...----....))))).-)).))))....- ( -26.40)
>DroYak_CAF1 41338 87 - 1
--------CUUACCCUGGCCUCCAUCUAGAUUCUUGAUU--CGGUGUAAAUCCAAUUAUUUUCGUCUAACCAAAAUUAGACGAAAAAAG------------------CCGGAUUU-
--------......(((((...............(((((--.(((....))).)))))(((((((((((......)))))))))))..)------------------))))....- ( -21.90)
>DroPer_CAF1 46180 104 - 1
UGUGUGGACUUUCUCUGGUUU-CAUCUUGAUUCUUGGUUUUGGGUGUAAAUCCAAUUAUUUUUGUCGAACCAAAACA--GCGAAAA-AAAAUUCAAGGAACAA-------AAAUG-
.(((.(((((......)))))-))).(((.(((((((..((((((....))))))...(((((((.(........).--)))))))-.....))))))).)))-------.....- ( -18.10)
>consensus
________CUUUCCCUGGUUUCCAUCUAGAUUCUUGAUU__CGGUGUAAAUCCAAUUAUUUUCGUCUAACCAAAAUUAGACGAAAAAAA____CACGGGAUGA____CCGGAUUU_
...............(((....((((..(((.....)))...)))).....)))....(((((((((((......))))))))))).............................. (-10.31 = -11.48 +   1.17)

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 10:20:56 2006