Locus 2140

Sequence ID 2R_DroMel_CAF1
Location 7,984,467 – 7,984,619
Length 152
Max. P 0.985716
window3544 window3545 window3546 window3547

overview

Window 4

Location 7,984,467 – 7,984,579
Length 112
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 71.80
Mean single sequence MFE -28.85
Consensus MFE -16.69
Energy contribution -16.95
Covariance contribution 0.25
Combinations/Pair 1.16
Mean z-score -1.91
Structure conservation index 0.58
SVM decision value 1.26
SVM RNA-class probability 0.937532
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7984467 112 + 20766785
AUGUUGAAAAAAAAA-----CAUUGUUCAUAGCUAGUUAAAAGCUGAAAAGUUGACAGCACUGGCUCAAGCAAUUCCCU-CUGACCAGUGCUGGAAAACACUCGCUGUCUUUUGAGCG
(((((........))-----))).(((((((((.(((....((((....))))..(((((((((.(((((.......))-.))))))))))))......))).)))).....))))). ( -32.10)
>DroSim_CAF1 21339 111 + 1
AUAUUGAAAA-AAAA-----CAUUUUUCAUAGCUAGUUAAAAGCUAAAAAGUUGACAGCACUGGCUCAAGCAAUUCCCU-CUGACCAGUGCUGGAAAACACUCGCUGUCUUUUGAGCG
....((((((-(...-----..)))))))(((((.......)))))....(((..(((((((((.(((((.......))-.))))))))))))...)))...((((........)))) ( -30.80)
>DroYak_CAF1 20964 111 + 1
AUUUUGGAUAGAAAA-----CAUAGUUCCCAGGUAGUUAUA-GCUAAAAAGUCGCCAGCACUGGCUUAAGCAGUUCCCU-GUGACCAGUGCUGGAAAACACUCGCUGUCUUUUGAGCG
...............-----....((((..((..(((....-(((....)))..((((((((((.....((((....))-))..)))))))))).........)))..))...)))). ( -30.80)
>DroAna_CAF1 20838 103 + 1
GUACAGAUAA-AUAGUGACUGAUUUUUAUUA------------U--UGUAGUUGGCAACACCAACUUAAGAGAUUCCCAGCUGUGUAGUGUUGAAAAACACCCGGUGUCUUUUGAGCG
.........(-(((((((.......))))))------------)--)((.(((((.....)))))(((((((((.....((((.(..(((((....))))))))))))))))))))). ( -21.70)
>consensus
AUAUUGAAAA_AAAA_____CAUUGUUCAUAGCUAGUUAAA_GCUAAAAAGUUGACAGCACUGGCUCAAGCAAUUCCCU_CUGACCAGUGCUGGAAAACACUCGCUGUCUUUUGAGCG
..................................................(((..(((((((((.(((.............))))))))))))...)))...((((........)))) (-16.69 = -16.95 +   0.25)

alignment

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secondary structure

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Window 5

Location 7,984,467 – 7,984,579
Length 112
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 71.80
Mean single sequence MFE -28.71
Consensus MFE -19.23
Energy contribution -18.85
Covariance contribution -0.38
Combinations/Pair 1.22
Mean z-score -1.92
Structure conservation index 0.67
SVM decision value 2.02
SVM RNA-class probability 0.985716
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7984467 112 - 20766785
CGCUCAAAAGACAGCGAGUGUUUUCCAGCACUGGUCAG-AGGGAAUUGCUUGAGCCAGUGCUGUCAACUUUUCAGCUUUUAACUAGCUAUGAACAAUG-----UUUUUUUUUCAACAU
.....((((((((.....(((((..((((((((((..(-((.......)))..))))))))))..........((((.......))))..))))).))-----))))))......... ( -30.70)
>DroSim_CAF1 21339 111 - 1
CGCUCAAAAGACAGCGAGUGUUUUCCAGCACUGGUCAG-AGGGAAUUGCUUGAGCCAGUGCUGUCAACUUUUUAGCUUUUAACUAGCUAUGAAAAAUG-----UUUU-UUUUCAAUAU
(((((..........))))).....((((((((((..(-((.......)))..)))))))))).........(((((.......)))))(((((((..-----...)-)))))).... ( -32.70)
>DroYak_CAF1 20964 111 - 1
CGCUCAAAAGACAGCGAGUGUUUUCCAGCACUGGUCAC-AGGGAACUGCUUAAGCCAGUGCUGGCGACUUUUUAGC-UAUAACUACCUGGGAACUAUG-----UUUUCUAUCCAAAAU
.(((.(((((...(((((....)))((((((((((..(-((....))).....))))))))))))..))))).)))-...........(..(((...)-----))..).......... ( -32.70)
>DroAna_CAF1 20838 103 - 1
CGCUCAAAAGACACCGGGUGUUUUUCAACACUACACAGCUGGGAAUCUCUUAAGUUGGUGUUGCCAACUACA--A------------UAAUAAAAAUCAGUCACUAU-UUAUCUGUAC
.........(((.((((.(((.............))).))))..........((((((.....))))))...--.------------............))).....-.......... ( -18.72)
>consensus
CGCUCAAAAGACAGCGAGUGUUUUCCAGCACUGGUCAG_AGGGAAUUGCUUAAGCCAGUGCUGUCAACUUUUUAGC_UUUAACUAGCUAUGAAAAAUG_____UUUU_UUUUCAAUAU
(((((..........))))).....((((((((((....(((......)))..))))))))))....................................................... (-19.23 = -18.85 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,984,500 – 7,984,619
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 81.40
Mean single sequence MFE -36.27
Consensus MFE -28.69
Energy contribution -29.19
Covariance contribution 0.50
Combinations/Pair 1.10
Mean z-score -1.84
Structure conservation index 0.79
SVM decision value 0.80
SVM RNA-class probability 0.854065
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7984500 119 + 20766785
AAAAGCUGAAAAGUUGACAGCACUGGCUCAAGCAAUUCCCU-CUGACCAGUGCUGGAAAACACUCGCUGUCUUUUGAGCGGCGCACGUGGAGCAAAAUCGAAGUGCUCACGUUUUUUUUU
...((((....))))..(((((((((.(((((.......))-.))))))))))))((((((...(((((((....)).)))))...(((.((((.........))))))))))))).... ( -38.10)
>DroSim_CAF1 21371 117 + 1
AAAAGCUAAAAAGUUGACAGCACUGGCUCAAGCAAUUCCCU-CUGACCAGUGCUGGAAAACACUCGCUGUCUUUUGAGCGGCGCACGUGGAGCAAAAUCGAAGUGCUCACGUUUU--UUU
....((......(((..(((((((((.(((((.......))-.))))))))))))...)))....((((((....)).))))))(((((.((((.........)))))))))...--... ( -37.70)
>DroYak_CAF1 20997 117 + 1
AUA-GCUAAAAAGUCGCCAGCACUGGCUUAAGCAGUUCCCU-GUGACCAGUGCUGGAAAACACUCGCUGUCUUUUGAGCGGCGCACGUGGAGCAAAAUCGAACUGCUCACGUUUU-UACU
...-((......((..((((((((((.....((((....))-))..))))))))))...))....((((((....)).))))))(((((.((((.........)))))))))...-.... ( -41.10)
>DroAna_CAF1 20868 113 + 1
-----U--UGUAGUUGGCAACACCAACUUAAGAGAUUCCCAGCUGUGUAGUGUUGAAAAACACCCGGUGUCUUUUGAGCGGCGCACGUGGAGCAAAACAGAAGAGCUCACGUUUUUAGUC
-----.--.((.(((((.....)))))(((((((((.....((((.(..(((((....)))))))))))))))))))))(((..(((((.(((...........)))))))).....))) ( -28.20)
>consensus
AAA_GCUAAAAAGUUGACAGCACUGGCUCAAGCAAUUCCCU_CUGACCAGUGCUGGAAAACACUCGCUGUCUUUUGAGCGGCGCACGUGGAGCAAAAUCGAAGUGCUCACGUUUU_UUUU
............(((..(((((((((.(((.............))))))))))))...)))...(((((((....)).))))).(((((.((((.........)))))))))........ (-28.69 = -29.19 +   0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,984,500 – 7,984,619
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 81.40
Mean single sequence MFE -36.41
Consensus MFE -30.49
Energy contribution -30.55
Covariance contribution 0.06
Combinations/Pair 1.10
Mean z-score -1.87
Structure conservation index 0.84
SVM decision value 0.99
SVM RNA-class probability 0.895461
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7984500 119 - 20766785
AAAAAAAAACGUGAGCACUUCGAUUUUGCUCCACGUGCGCCGCUCAAAAGACAGCGAGUGUUUUCCAGCACUGGUCAG-AGGGAAUUGCUUGAGCCAGUGCUGUCAACUUUUCAGCUUUU
........(((((((((.........)))).)))))((((((((........)))).))))....((((((((((..(-((.......)))..))))))))))................. ( -37.90)
>DroSim_CAF1 21371 117 - 1
AAA--AAAACGUGAGCACUUCGAUUUUGCUCCACGUGCGCCGCUCAAAAGACAGCGAGUGUUUUCCAGCACUGGUCAG-AGGGAAUUGCUUGAGCCAGUGCUGUCAACUUUUUAGCUUUU
...--...(((((((((.........)))).)))))((((((((........)))).))))....((((((((((..(-((.......)))..))))))))))................. ( -37.90)
>DroYak_CAF1 20997 117 - 1
AGUA-AAAACGUGAGCAGUUCGAUUUUGCUCCACGUGCGCCGCUCAAAAGACAGCGAGUGUUUUCCAGCACUGGUCAC-AGGGAACUGCUUAAGCCAGUGCUGGCGACUUUUUAGC-UAU
(((.-(((((((((((((.......))))).)))))((((((((........)))).))))...(((((((((((..(-((....))).....)))))))))))......))).))-).. ( -43.70)
>DroAna_CAF1 20868 113 - 1
GACUAAAAACGUGAGCUCUUCUGUUUUGCUCCACGUGCGCCGCUCAAAAGACACCGGGUGUUUUUCAACACUACACAGCUGGGAAUCUCUUAAGUUGGUGUUGCCAACUACA--A-----
........((((((((...........))).)))))((((((((.((.(((..((((.(((.............))).))))...))).)).)).))))))...........--.----- ( -26.12)
>consensus
AAAA_AAAACGUGAGCACUUCGAUUUUGCUCCACGUGCGCCGCUCAAAAGACAGCGAGUGUUUUCCAGCACUGGUCAG_AGGGAAUUGCUUAAGCCAGUGCUGUCAACUUUUUAGC_UUU
........((((((((...........))).)))))((((((((........)))).))))....((((((((((....(((......)))..))))))))))................. (-30.49 = -30.55 +   0.06)

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 10:22:22 2006