Locus 3107

Sequence ID 3R_DroMel_CAF1
Location 8,195,506 – 8,195,690
Length 184
Max. P 0.815535
window5040 window5041 window5042

overview

Window 0

Location 8,195,506 – 8,195,621
Length 115
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.07
Mean single sequence MFE -27.55
Consensus MFE -18.14
Energy contribution -18.32
Covariance contribution 0.19
Combinations/Pair 1.26
Mean z-score -1.74
Structure conservation index 0.66
SVM decision value 0.20
SVM RNA-class probability 0.629159
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8195506 115 - 27905053
AAAAGA---AUUUAUGUUUUUUCAGGCGCACAGAUGUUCAUUAGAAAUGCAAAAUUGUGUUUCA-AGCUAAUCGAUUGCA-UGCUUAUGUGUUUGCUAAUCUUAGCAAGUCGAUGUGUAA
.(((((---((....)))))))...(((((..(((........((((((((....)))))))).-.(((((..(((((((-.((......)).))).)))))))))..)))..))))).. ( -27.50)
>DroSim_CAF1 9776 115 - 1
AAAAGAAGAAUUUA----UUUUCAGGCGCGCAGAUGUUCAUUAGAAAUGCAAAAAUGUGUUUCA-AGCAAAUCGAGUGCACUGCGCAUGUGUUUGCCAACUUUAGCAAGUCGAAGUGUAA
....(((((.....----))))).(((((((((..........((((((((....)))))))).-.(((.......))).))))))......((((........)))))))......... ( -28.00)
>DroEre_CAF1 11029 114 - 1
AGAGAGAGAAUUUA----UUUUCAGGCGCACAGAUGUUCAUAAGAAAUGCAAAAAUGUGUUUCAAAGCAAAUUGAGUGCAC--CAAAUGGGUGUGUCAGCUUUAGCAAGUCGAAGUGUAA
.....(((((....----)))))..((((...(((........((((((((....))))))))(((((....(((.(((((--(.....)))))))))))))).....)))...)))).. ( -25.50)
>DroYak_CAF1 9582 112 - 1
AUAAGAAGAAUUUA----UUUUCAGGCGCACAGAUGUUCAUUAGAAAUGCAAAAAUGUGUUUCA-AGCAAAUUGAGUGCAC--CAAAUGGGUGUGCCAACU-UAGCAAGUCGAGGUGUUA
....(((((.....----))))).(((((...(((........((((((((....)))))))).-.((((.(((.(..(((--(.....))))..)))).)-).))..)))...))))). ( -29.20)
>consensus
AAAAGAAGAAUUUA____UUUUCAGGCGCACAGAUGUUCAUUAGAAAUGCAAAAAUGUGUUUCA_AGCAAAUCGAGUGCAC__CAAAUGGGUGUGCCAACUUUAGCAAGUCGAAGUGUAA
........................(((((((............((((((((....))))))))...(((.......)))...........))))))).(((((........))))).... (-18.14 = -18.32 +   0.19)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,195,584 – 8,195,690
Length 106
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.36
Mean single sequence MFE -16.69
Consensus MFE -10.89
Energy contribution -11.33
Covariance contribution 0.45
Combinations/Pair 1.06
Mean z-score -1.83
Structure conservation index 0.65
SVM decision value 0.66
SVM RNA-class probability 0.815535
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8195584 106 + 27905053
UGAACAUCUGUGCGCCUGAAAAAACAUAAAU---UCUUUUAAAAUGCAAAAAAAAAUAAGUA---------CAAACAAAUAAGCAGGCAAACAGAAACCAGAUAAGAAU--UCAAGCCGG
......(((((..(((((........((((.---...))))..................((.---------...)).......)))))..)))))..............--......... ( -13.90)
>DroSim_CAF1 9855 104 + 1
UGAACAUCUGCGCGCCUGAAAA----UAAAUUCUUCUUUUAAAAUGCAAA---AAAUAAGUA---------CAAACAUACAAACAGGCAAACAGAAAGCAGAUAAGAAUUUUCAGGCCGG
..........((.(((((((((----(....(((.(((((....(((...---......(((---------......)))......)))....))))).))).....)))))))))))). ( -22.16)
>DroEre_CAF1 11107 111 + 1
UGAACAUCUGUGCGCCUGAAAA----UAAAUUCUCUCUCUAAAAUGCAAA---AAGUAAGCAAAUAAAUAAUAAGUAAAUAAACAGGCAAACAGAAAGCAGAUAACAAU--UCAAGCCGG
......(((((..(((((....----..................(((...---......))).....((.....)).......)))))..)))))..............--......... ( -14.00)
>consensus
UGAACAUCUGUGCGCCUGAAAA____UAAAUUCUUCUUUUAAAAUGCAAA___AAAUAAGUA_________CAAACAAAUAAACAGGCAAACAGAAAGCAGAUAAGAAU__UCAAGCCGG
......(((((..(((((........((((.......))))...(((............))).....................)))))..)))))......................... (-10.89 = -11.33 +   0.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 8,195,584 – 8,195,690
Length 106
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.36
Mean single sequence MFE -21.09
Consensus MFE -12.67
Energy contribution -12.45
Covariance contribution -0.22
Combinations/Pair 1.09
Mean z-score -1.71
Structure conservation index 0.60
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8195584 106 - 27905053
CCGGCUUGA--AUUCUUAUCUGGUUUCUGUUUGCCUGCUUAUUUGUUUG---------UACUUAUUUUUUUUUGCAUUUUAAAAGA---AUUUAUGUUUUUUCAGGCGCACAGAUGUUCA
((((..(((--....))).))))..(((((.((((((............---------.((.((..((((((((.....)))))))---)..)).)).....)))))).)))))...... ( -18.97)
>DroSim_CAF1 9855 104 - 1
CCGGCCUGAAAAUUCUUAUCUGCUUUCUGUUUGCCUGUUUGUAUGUUUG---------UACUUAUUU---UUUGCAUUUUAAAAGAAGAAUUUA----UUUUCAGGCGCGCAGAUGUUCA
.((((((((((((.....(((.((((..(..(((..((..((((....)---------)))..))..---...)))..)..)))).)))....)----))))))))).)).......... ( -24.20)
>DroEre_CAF1 11107 111 - 1
CCGGCUUGA--AUUGUUAUCUGCUUUCUGUUUGCCUGUUUAUUUACUUAUUAUUUAUUUGCUUACUU---UUUGCAUUUUAGAGAGAGAAUUUA----UUUUCAGGCGCACAGAUGUUCA
..(((..((--.......)).))).(((((.((((((...............((((..(((......---...)))...))))...........----....)))))).)))))...... ( -20.11)
>consensus
CCGGCUUGA__AUUCUUAUCUGCUUUCUGUUUGCCUGUUUAUUUGUUUG_________UACUUAUUU___UUUGCAUUUUAAAAGAAGAAUUUA____UUUUCAGGCGCACAGAUGUUCA
.........................(((((.((((((.................................................................)))))).)))))...... (-12.67 = -12.45 +  -0.22)

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 10:53:15 2006