Locus 3632

Sequence ID 2R_DroMel_CAF1
Location 12,029,580 – 12,029,703
Length 123
Max. P 0.989428
window5909 window5910 window5911 window5912

overview

Window 9

Location 12,029,580 – 12,029,679
Length 99
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 76.64
Mean single sequence MFE -26.82
Consensus MFE -18.54
Energy contribution -17.98
Covariance contribution -0.55
Combinations/Pair 1.19
Mean z-score -2.15
Structure conservation index 0.69
SVM decision value 1.76
SVM RNA-class probability 0.976091
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12029580 99 + 20766785
UGUUUG---------UGUACGUGUUGGGGCAUACGCG-----CUGUG-----CAAAGUGCGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCCUUU--GUUGAAAGUUGACAUUG
((((.(---------(((((.((((((.((....)).-----))).)-----))..)))))).......((((.(((..((((((((.....)))))))).--..))).))))))))... ( -28.30)
>DroVir_CAF1 32632 103 + 1
UGUGU-------UCUGGUACGUGUCAAAGCGCACACA-----GUGUGCCC---AAAGUGCGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCCUUU--GUUGAAAGUUGACAUUG
.....-------........(((((..(((((((...-----.((....)---)..)))))))......((((.(((..((((((((.....)))))))).--..))).))))))))).. ( -31.10)
>DroGri_CAF1 32928 92 + 1
UGUUUGUCAAAAAGUAGUACGUGUCAAAGC--------------G------------UCAGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCCUUU--GUUGAAAGUUGACAUUG
....((((((........((((......))--------------)------------)(((((......)))))(((..((((((((.....)))))))).--..)))...))))))... ( -24.80)
>DroWil_CAF1 39602 101 + 1
-----C---------UGUACGUGUCAAAGCAUACGCAUGCAGUAGAG-----AGAAGUGCGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCCUUUUGUUUGAAAGUUGACAUUG
-----.---------.....(((((........(((((.(......)-----....)))))........((((.(((..((((((((.....)))))))).....))).))))))))).. ( -23.20)
>DroMoj_CAF1 39586 97 + 1
UGUAU-------UGUGGUACGUGUCAAA--------------GUGUGCCCCGAGAAGUGCGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCCUUU--GUUGAAAGUUGACAUUG
.((((-------....))))(((((..(--------------(((..(........)..))))......((((.(((..((((((((.....)))))))).--..))).))))))))).. ( -28.50)
>DroPer_CAF1 79083 99 + 1
UGUUUG---------UGUACGUGUCAAAGCAUACGCG-----UUGUG-----CAAAGUGCGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCUUUU--GUUGAAAGUUGACAUUG
((((.(---------(((((.((((((.((....)).-----))).)-----))..)))))).......((((.(((..((((((((.....)))))))).--..))).))))))))... ( -25.00)
>consensus
UGUUUG_________UGUACGUGUCAAAGCAUACGC______GUGUG______AAAGUGCGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCCUUU__GUUGAAAGUUGACAUUG
....................(((((((.................................(((......)))..(((..((((((((.....)))))))).....)))...))))))).. (-18.54 = -17.98 +  -0.55)

alignment

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secondary structure

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Window 0

Location 12,029,580 – 12,029,679
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.64
Mean single sequence MFE -21.67
Consensus MFE -15.33
Energy contribution -16.00
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -2.77
Structure conservation index 0.71
SVM decision value 2.16
SVM RNA-class probability 0.989428
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12029580 99 - 20766785
CAAUGUCAACUUUCAAC--AAAGGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCGCACUUUG-----CACAG-----CGCGUAUGCCCCAACACGUACA---------CAAACA
...(((((.........--.((((((((.....))))))))..)))))..........((((......-----....)-----)))(((((........))))).---------...... ( -21.30)
>DroVir_CAF1 32632 103 - 1
CAAUGUCAACUUUCAAC--AAAGGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCGCACUUU---GGGCACAC-----UGUGUGCGCUUUGACACGUACCAGA-------ACACA
...((((((((.(((..--.((((((((.....))))))))..))).))........(((((((..(---((.....)-----)).))))))))))))).........-------..... ( -28.80)
>DroGri_CAF1 32928 92 - 1
CAAUGUCAACUUUCAAC--AAAGGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCUGA------------C--------------GCUUUGACACGUACUACUUUUUGACAAACA
...((((((...(((..--.((((((((.....))))))))..)))(((((......)))))(------------(--------------(........)))........)))))).... ( -23.00)
>DroWil_CAF1 39602 101 - 1
CAAUGUCAACUUUCAAACAAAAGGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCGCACUUCU-----CUCUACUGCAUGCGUAUGCUUUGACACGUACA---------G-----
...((((((...........((((((((.....)))))))).(((.(((((......)))(((.....-----......))).))))).....))))))......---------.----- ( -20.10)
>DroMoj_CAF1 39586 97 - 1
CAAUGUCAACUUUCAAC--AAAGGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCGCACUUCUCGGGGCACAC--------------UUUGACACGUACCACA-------AUACA
...((((((...(((..--.((((((((.....))))))))..)))..(((......)))((.((.....))))....--------------.)))))).(((.....-------.))). ( -20.30)
>DroPer_CAF1 79083 99 - 1
CAAUGUCAACUUUCAAC--AAAAGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCGCACUUUG-----CACAA-----CGCGUAUGCUUUGACACGUACA---------CAAACA
...((((((........--....(((((.....)))))..........(((......)))(((...((-----(....-----.)))..))).))))))......---------...... ( -16.50)
>consensus
CAAUGUCAACUUUCAAC__AAAGGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCGCACUUU______CACAA______GCGUAUGCUUUGACACGUACA_________CAAACA
...((((((...........((((((((.....)))))))).......(((......))).................................))))))..................... (-15.33 = -16.00 +   0.67)

alignment

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secondary structure

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Window 1

Location 12,029,608 – 12,029,703
Length 95
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.93
Mean single sequence MFE -23.98
Consensus MFE -17.11
Energy contribution -17.09
Covariance contribution -0.03
Combinations/Pair 1.10
Mean z-score -1.60
Structure conservation index 0.71
SVM decision value 0.79
SVM RNA-class probability 0.851756
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12029608 95 + 20766785
--CUGUG-----CAAAGUGCGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCCUUU--GUUGAAAGUUGACAUUGUGUGAAAGAAACGUU------------UGCG-AAAA---C
--...((-----((((((((((.......((((.(((..((((((((.....)))))))).--..))).))))......)))).......)).))------------))))-....---. ( -22.83)
>DroVir_CAF1 32662 108 + 1
--GUGUGCCC---AAAGUGCGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCCUUU--GUUGAAAGUUGACAUUGUGUAA-AGAAACGUUUUGCUACUGUACUGCG-AAAA---C
--(((..(..---...)..))).......((((.(((..((((((((.....)))))))).--..))).))))............-.....(((..(((....)))..)))-....---. ( -25.20)
>DroGri_CAF1 32958 98 + 1
----G------------UCAGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCCUUU--GUUGAAAGUUGACAUUGUGUAA-AGAAAACGUUUGCUGCUG--CUGCG-AAAAAUAC
----(------------((((((...........(((..((((((((.....)))))))).--..))).))))))).........-......(((..((....)--).)))-........ ( -22.90)
>DroWil_CAF1 39628 100 + 1
AGUAGAG-----AGAAGUGCGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCCUUUUGUUUGAAAGUUGACAUUGUGUAAAGAAAACGUU------------UUGGCGCAA---C
.......-----.....(((((((((...((((.(((..((((((((.....)))))))).....))).)))).((.....))...........)------------)))))))).---. ( -25.00)
>DroMoj_CAF1 39607 110 + 1
--GUGUGCCCCGAGAAGUGCGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCCUUU--GUUGAAAGUUGACAUUGUGUAA-GGAAACAUUUUGCUGCUGUA-UGCG-AAAA---C
--((((((..((.(((((((((.......((((.(((..((((((((.....)))))))).--..))).))))......))))..-(....))))))..))..)))-))).-....---. ( -27.82)
>DroPer_CAF1 79111 95 + 1
--UUGUG-----CAAAGUGCGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCUUUU--GUUGAAAGUUGACAUUGUGUGAAAGAAACGUU------------UGCG-AAAA---C
--...((-----((((((((((.......((((.(((..((((((((.....)))))))).--..))).))))......)))).......)).))------------))))-....---. ( -20.13)
>consensus
__GUGUG______AAAGUGCGCUAAAUUAAGCUGUCAUUAAGGACUUAAUUAAAGUCCUUU__GUUGAAAGUUGACAUUGUGUAA_AGAAACGUU____________UGCG_AAAA___C
.................(((((.......((((.(((..((((((((.....)))))))).....))).))))......))))).................................... (-17.11 = -17.09 +  -0.03)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,029,608 – 12,029,703
Length 95
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.93
Mean single sequence MFE -18.62
Consensus MFE -12.89
Energy contribution -13.06
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.69
SVM decision value 0.88
SVM RNA-class probability 0.873057
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12029608 95 - 20766785
G---UUUU-CGCA------------AACGUUUCUUUCACACAAUGUCAACUUUCAAC--AAAGGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCGCACUUUG-----CACAG--
.---....-.(((------------((.((.............(((((.........--.((((((((.....))))))))..)))))(((......)))..))))))-----)....-- ( -19.30)
>DroVir_CAF1 32662 108 - 1
G---UUUU-CGCAGUACAGUAGCAAAACGUUUCU-UUACACAAUGUCAACUUUCAAC--AAAGGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCGCACUUU---GGGCACAC--
.---....-.((.(((.((.(((.....))).))-.))).(((.(((.....(((..--.((((((((.....))))))))..)))..(((......)))).)).))---).))....-- ( -21.00)
>DroGri_CAF1 32958 98 - 1
GUAUUUUU-CGCAG--CAGCAGCAAACGUUUUCU-UUACACAAUGUCAACUUUCAAC--AAAGGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCUGA------------C----
(((.....-((..(--(....))...))......-.))).............(((..--.((((((((.....))))))))..)))(((((......))))).------------.---- ( -18.40)
>DroWil_CAF1 39628 100 - 1
G---UUGCGCCAA------------AACGUUUUCUUUACACAAUGUCAACUUUCAAACAAAAGGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCGCACUUCU-----CUCUACU
.---.(((((.((------------(..((.......))....(((((............((((((((.....))))))))..)))))......))).))))).....-----....... ( -18.54)
>DroMoj_CAF1 39607 110 - 1
G---UUUU-CGCA-UACAGCAGCAAAAUGUUUCC-UUACACAAUGUCAACUUUCAAC--AAAGGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCGCACUUCUCGGGGCACAC--
.---....-.((.-....)).......(((.(((-(.......(((((.........--.((((((((.....))))))))..)))))(((......))).........)))).))).-- ( -20.60)
>DroPer_CAF1 79111 95 - 1
G---UUUU-CGCA------------AACGUUUCUUUCACACAAUGUCAACUUUCAAC--AAAAGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCGCACUUUG-----CACAA--
.---....-.(((------------((.((.............(((((..(((....--.)))(((((.....))))).....)))))(((......)))..))))))-----)....-- ( -13.90)
>consensus
G___UUUU_CGCA____________AACGUUUCU_UUACACAAUGUCAACUUUCAAC__AAAGGACUUUAAUUAAGUCCUUAAUGACAGCUUAAUUUAGCGCACUUU______CACAA__
...........................................(((((............((((((((.....))))))))..)))))(((......))).................... (-12.89 = -13.06 +   0.17)

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 11:00:22 2006