Locus 1352

Sequence ID 2R_DroMel_CAF1
Location 5,227,389 – 5,227,515
Length 126
Max. P 0.849436
window2335 window2336 window2337 window2338

overview

Window 5

Location 5,227,389 – 5,227,483
Length 94
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 81.63
Mean single sequence MFE -28.35
Consensus MFE -19.76
Energy contribution -19.68
Covariance contribution -0.08
Combinations/Pair 1.29
Mean z-score -2.27
Structure conservation index 0.70
SVM decision value 0.78
SVM RNA-class probability 0.849436
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5227389 94 + 20766785
GGGAGAGUAGAAUUGAGUUUUGUCUUGCAUAUUAAGGGCGCCAAAACGAUGCCCCAAUAAGCCGCAUUUCGGCUCAUUGCUGCUUUGUUUUUGC
(.((((.((((((...)))))))))).)...........((.(((((((.((..((((.(((((.....))))).))))..)).))))))).)) ( -24.90)
>DroSec_CAF1 103132 94 + 1
GCCAGAGCAGAAUUGAGUUUUGUCUUGCACAUUAAGGGAGCCAAAACGAUGCCCCAAUAAGCCGCAUUUCGGCUCAUUGCUGCUUUGUUUUUGC
..((((((((......((((((.(((.(.......).))).)))))).......((((.(((((.....))))).))))))))))))....... ( -29.00)
>DroSim_CAF1 89293 94 + 1
GGCAGAGCAGAAUUGAGUUUUGUCUUGCACAUUACGGGAGCCAAAACGAUGCCCCAAUAAGCCGCAUUUCGGCUCAUUGCUGCUUUGUUUUUAC
((((((((((......((((((.(((.(.......).))).)))))).......((((.(((((.....))))).))))))))))))))..... ( -30.70)
>DroEre_CAF1 104032 94 + 1
GGCAGAGCAGUACUGAGUUUUGCCCUGCACAUUUAGGGCGCUAAAACGAUGCUCCAAUAAGCCGCAUUUUGGCUUAUUGCUGCCUUGUUUUUUC
(((((((((......(((...((((((......))))))))).......)))))((((((((((.....)))))))))).)))).......... ( -34.92)
>DroYak_CAF1 102249 94 + 1
GGCAGAGUAAAAUUGAGUUUUGUCCUGCACAUUAAGGGCGCUAAAACGAUGCCCCAAUAAGCCGUACUUUGGCUCAUUGCUGCUUUGUUUUUUC
.((((..((((((...))))))..))))..............(((((((.((..((((.(((((.....))))).))))..)).)))))))... ( -25.40)
>DroAna_CAF1 121039 93 + 1
AACAGAACAGACAUGAAUUUUGAAUUGAAUUCUAAAGGAGCUAGAACGACGCCACAAUCGGCUUAA-AUUAACUGAUUGUGGCCUUGUUUUUUC
..............((((((......))))))..........(((((((.(((((((((((.....-.....))))))))))).)))))))... ( -25.20)
>consensus
GGCAGAGCAGAAUUGAGUUUUGUCUUGCACAUUAAGGGAGCCAAAACGAUGCCCCAAUAAGCCGCAUUUCGGCUCAUUGCUGCUUUGUUUUUUC
.((((..((((((...))))))..))))..............(((((((.((..((((.(((((.....))))).))))..)).)))))))... (-19.76 = -19.68 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,227,389 – 5,227,483
Length 94
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 81.63
Mean single sequence MFE -27.12
Consensus MFE -16.61
Energy contribution -16.37
Covariance contribution -0.25
Combinations/Pair 1.33
Mean z-score -2.48
Structure conservation index 0.61
SVM decision value 0.66
SVM RNA-class probability 0.813593
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5227389 94 - 20766785
GCAAAAACAAAGCAGCAAUGAGCCGAAAUGCGGCUUAUUGGGGCAUCGUUUUGGCGCCCUUAAUAUGCAAGACAAAACUCAAUUCUACUCUCCC
...........(((.((((((((((.....))))))))))((((..(.....)..))))......))).......................... ( -25.50)
>DroSec_CAF1 103132 94 - 1
GCAAAAACAAAGCAGCAAUGAGCCGAAAUGCGGCUUAUUGGGGCAUCGUUUUGGCUCCCUUAAUGUGCAAGACAAAACUCAAUUCUGCUCUGGC
.......((.(((((((((((((((.....))))))))))..(((.((((..((...))..)))))))................))))).)).. ( -29.20)
>DroSim_CAF1 89293 94 - 1
GUAAAAACAAAGCAGCAAUGAGCCGAAAUGCGGCUUAUUGGGGCAUCGUUUUGGCUCCCGUAAUGUGCAAGACAAAACUCAAUUCUGCUCUGCC
.......((.(((((((((((((((.....))))))))))..(((.((((.(((...))).)))))))................))))).)).. ( -28.30)
>DroEre_CAF1 104032 94 - 1
GAAAAAACAAGGCAGCAAUAAGCCAAAAUGCGGCUUAUUGGAGCAUCGUUUUAGCGCCCUAAAUGUGCAGGGCAAAACUCAGUACUGCUCUGCC
..........((((.(((((((((.......)))))))))(((((..((....))(((((........)))))............))))))))) ( -32.10)
>DroYak_CAF1 102249 94 - 1
GAAAAAACAAAGCAGCAAUGAGCCAAAGUACGGCUUAUUGGGGCAUCGUUUUAGCGCCCUUAAUGUGCAGGACAAAACUCAAUUUUACUCUGCC
...........(((((((((((((.......)))))))))(((....(((((.((((.......)))))))))....))).........)))). ( -24.90)
>DroAna_CAF1 121039 93 - 1
GAAAAAACAAGGCCACAAUCAGUUAAU-UUAAGCCGAUUGUGGCGUCGUUCUAGCUCCUUUAGAAUUCAAUUCAAAAUUCAUGUCUGUUCUGUU
(((...(((..(((((((((.(((...-...))).)))))))))...(((((((.....)))))))...............)))...))).... ( -22.70)
>consensus
GAAAAAACAAAGCAGCAAUGAGCCAAAAUGCGGCUUAUUGGGGCAUCGUUUUAGCGCCCUUAAUGUGCAAGACAAAACUCAAUUCUGCUCUGCC
...........((..(((((((((.......)))))))))..))...(((((.((...........)))))))..................... (-16.61 = -16.37 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,227,423 – 5,227,515
Length 92
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 83.17
Mean single sequence MFE -26.12
Consensus MFE -18.25
Energy contribution -17.92
Covariance contribution -0.33
Combinations/Pair 1.24
Mean z-score -2.96
Structure conservation index 0.70
SVM decision value 0.78
SVM RNA-class probability 0.848048
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5227423 92 + 20766785
AGGGCGCCAAAACGAUGCCCCAAUAAGCCGCAUUUCGGCUCAUUGCUGCUUUGUUUUUGCGACCUACUAACAUUGU--AACCAAUUCGACCAGU
.((((((.(((((((.((..((((.(((((.....))))).))))..)).))))))).))).)))...........--................ ( -27.40)
>DroSec_CAF1 103166 92 + 1
AGGGAGCCAAAACGAUGCCCCAAUAAGCCGCAUUUCGGCUCAUUGCUGCUUUGUUUUUGCGACCUACUAACAUUGU--AAUCUAUUCGACCAGU
(((..((.(((((((.((..((((.(((((.....))))).))))..)).))))))).))..)))...........--................ ( -26.80)
>DroSim_CAF1 89327 92 + 1
CGGGAGCCAAAACGAUGCCCCAAUAAGCCGCAUUUCGGCUCAUUGCUGCUUUGUUUUUACGACCUACUAACAUUGU--AAUCUAUUCGACCAGU
.((..(..(((((((.((..((((.(((((.....))))).))))..)).)))))))..)..))............--................ ( -21.80)
>DroEre_CAF1 104066 92 + 1
AGGGCGCUAAAACGAUGCUCCAAUAAGCCGCAUUUUGGCUUAUUGCUGCCUUGUUUUUUCGACCCACUAACAUUGU--AACCAAUUCGACCAGU
.(((((..(((((((.((..((((((((((.....))))))))))..)).)))))))..)).)))...........--................ ( -30.10)
>DroYak_CAF1 102283 92 + 1
AGGGCGCUAAAACGAUGCCCCAAUAAGCCGUACUUUGGCUCAUUGCUGCUUUGUUUUUUCGACCUACUAAAAUUGU--ACCAAAUUCGACCAGU
.(((((..(((((((.((..((((.(((((.....))))).))))..)).)))))))..)).)))...........--................ ( -23.60)
>DroAna_CAF1 121073 93 + 1
AAGGAGCUAGAACGACGCCACAAUCGGCUUAA-AUUAACUGAUUGUGGCCUUGUUUUUUCGUCCACCUAAAAUUAAUUCCUUAAUUCGACCAGU
..((((..(((((((.(((((((((((.....-.....))))))))))).)))))))..).))).............................. ( -27.00)
>consensus
AGGGAGCCAAAACGAUGCCCCAAUAAGCCGCAUUUCGGCUCAUUGCUGCUUUGUUUUUUCGACCUACUAACAUUGU__AACCAAUUCGACCAGU
.(((....(((((((.((..((((.(((((.....))))).))))..)).))))))).....)))............................. (-18.25 = -17.92 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,227,423 – 5,227,515
Length 92
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 83.17
Mean single sequence MFE -27.97
Consensus MFE -18.29
Energy contribution -17.68
Covariance contribution -0.61
Combinations/Pair 1.26
Mean z-score -2.21
Structure conservation index 0.65
SVM decision value 0.18
SVM RNA-class probability 0.621858
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5227423 92 - 20766785
ACUGGUCGAAUUGGUU--ACAAUGUUAGUAGGUCGCAAAAACAAAGCAGCAAUGAGCCGAAAUGCGGCUUAUUGGGGCAUCGUUUUGGCGCCCU
(((((....((((...--.)))).)))))(((.(((.(((((...((..((((((((((.....))))))))))..))...))))).))).))) ( -32.30)
>DroSec_CAF1 103166 92 - 1
ACUGGUCGAAUAGAUU--ACAAUGUUAGUAGGUCGCAAAAACAAAGCAGCAAUGAGCCGAAAUGCGGCUUAUUGGGGCAUCGUUUUGGCUCCCU
..(((((.....))))--)..........(((..((.(((((...((..((((((((((.....))))))))))..))...))))).))..))) ( -28.80)
>DroSim_CAF1 89327 92 - 1
ACUGGUCGAAUAGAUU--ACAAUGUUAGUAGGUCGUAAAAACAAAGCAGCAAUGAGCCGAAAUGCGGCUUAUUGGGGCAUCGUUUUGGCUCCCG
..(((((.....))))--)...........((..((.(((((...((..((((((((((.....))))))))))..))...))))).))..)). ( -27.40)
>DroEre_CAF1 104066 92 - 1
ACUGGUCGAAUUGGUU--ACAAUGUUAGUGGGUCGAAAAAACAAGGCAGCAAUAAGCCAAAAUGCGGCUUAUUGGAGCAUCGUUUUAGCGCCCU
(((((....((((...--.)))).)))))(((.((..(((((...((..(((((((((.......)))))))))..))...)))))..))))). ( -29.50)
>DroYak_CAF1 102283 92 - 1
ACUGGUCGAAUUUGGU--ACAAUUUUAGUAGGUCGAAAAAACAAAGCAGCAAUGAGCCAAAGUACGGCUUAUUGGGGCAUCGUUUUAGCGCCCU
((..(......)..))--...........(((.((..(((((...((..(((((((((.......)))))))))..))...)))))..)).))) ( -25.10)
>DroAna_CAF1 121073 93 - 1
ACUGGUCGAAUUAAGGAAUUAAUUUUAGGUGGACGAAAAAACAAGGCCACAAUCAGUUAAU-UUAAGCCGAUUGUGGCGUCGUUCUAGCUCCUU
(((....(((((((....)))))))..)))(((.(....(((.(.(((((((((.(((...-...))).))))))))).).)))....)))).. ( -24.70)
>consensus
ACUGGUCGAAUUGAUU__ACAAUGUUAGUAGGUCGAAAAAACAAAGCAGCAAUGAGCCAAAAUGCGGCUUAUUGGGGCAUCGUUUUAGCGCCCU
..............................((..(..(((((...((..(((((((((.......)))))))))..))...)))))..)..)). (-18.29 = -17.68 +  -0.61)

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 10:02:54 2006