Locus 7081

Sequence ID 3L_DroMel_CAF1
Location 19,143,269 – 19,143,428
Length 159
Max. P 0.997424
window11484 window11485 window11486

overview

Window 4

Location 19,143,269 – 19,143,389
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.67
Mean single sequence MFE -27.58
Consensus MFE -27.40
Energy contribution -27.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.82
Structure conservation index 0.99
SVM decision value 1.89
SVM RNA-class probability 0.981565
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19143269 120 + 23771897
GAGCCAUCGAAGGGAAUUUAUAAUUAAUAAAUGCCCCCAAGUGAGGCAGUGAGAACAAGUGCUGAUUAGUGCAAUGACAAAGCAAUCAAAACACUUUGGCAAACGUGGCAAUUAAAAUUC
..((((.((..(((.((((((.....)))))).)))(((((((.((((.(.......).))))(((...(((.........))))))....))).))))....))))))........... ( -27.40)
>DroSec_CAF1 6182 120 + 1
GAGCCAUCGAAGGGAAUUUAUAAUUAAUAAAUGCCCCCAAGUGAGGCAGUGAGAACAAGUGCUGAUUAGUGCAAUGACAAAGCAAUCAAAACACUUUGGCAAACGUGGCAAUUAAAAUUC
..((((.((..(((.((((((.....)))))).)))(((((((.((((.(.......).))))(((...(((.........))))))....))).))))....))))))........... ( -27.40)
>DroSim_CAF1 5752 120 + 1
GAGCCAUCGAAGGGAAUUUAUAAUUAAUAAAUGCCCCCAAGUGAGGCAGUGAGAACAAGUGCUGAUUAGUGCAAUGACAAAGCAAUCAAAACACUUUGGCAAACGUGGCAAUUAAAAUUC
..((((.((..(((.((((((.....)))))).)))(((((((.((((.(.......).))))(((...(((.........))))))....))).))))....))))))........... ( -27.40)
>DroEre_CAF1 6637 120 + 1
GAGCCACCGAAGGGAAUUUAUAAUUAAUAAAUGCCCCCAAGUGAGGCAGUGAGAACAAGUGCUGAUUAGUGCAAUGACAAAGCAAUCAAAACACUUUGGCAAACGUGGCAAUUAAAAUUC
..(((((....(((.((((((.....)))))).)))(((((((.((((.(.......).))))(((...(((.........))))))....))).)))).....)))))........... ( -28.30)
>DroYak_CAF1 6543 120 + 1
GAGCCAUCGAAGGGAAUUUAUAAUUAAUAAAUGCCCCCAAGUGAGGCAGUGAGAACAAGUGCUGAUUAGUGCAAUGACAAAGCAAUCAAAACACUUUGGCAAACGUGGCAAUUAAAAUUC
..((((.((..(((.((((((.....)))))).)))(((((((.((((.(.......).))))(((...(((.........))))))....))).))))....))))))........... ( -27.40)
>consensus
GAGCCAUCGAAGGGAAUUUAUAAUUAAUAAAUGCCCCCAAGUGAGGCAGUGAGAACAAGUGCUGAUUAGUGCAAUGACAAAGCAAUCAAAACACUUUGGCAAACGUGGCAAUUAAAAUUC
..((((.((..(((.((((((.....)))))).)))(((((((.((((.(.......).))))(((...(((.........))))))....))).))))....))))))........... (-27.40 = -27.40 +   0.00)

alignment

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secondary structure

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Window 5

Location 19,143,269 – 19,143,389
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.67
Mean single sequence MFE -28.88
Consensus MFE -28.40
Energy contribution -28.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.98
SVM decision value 2.86
SVM RNA-class probability 0.997424
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19143269 120 - 23771897
GAAUUUUAAUUGCCACGUUUGCCAAAGUGUUUUGAUUGCUUUGUCAUUGCACUAAUCAGCACUUGUUCUCACUGCCUCACUUGGGGGCAUUUAUUAAUUAUAAAUUCCCUUCGAUGGCUC
...........((((((....(((((((((..((((......))))..))))).....(((..((....)).))).....))))(((.((((((.....)))))).)))..)).)))).. ( -28.40)
>DroSec_CAF1 6182 120 - 1
GAAUUUUAAUUGCCACGUUUGCCAAAGUGUUUUGAUUGCUUUGUCAUUGCACUAAUCAGCACUUGUUCUCACUGCCUCACUUGGGGGCAUUUAUUAAUUAUAAAUUCCCUUCGAUGGCUC
...........((((((....(((((((((..((((......))))..))))).....(((..((....)).))).....))))(((.((((((.....)))))).)))..)).)))).. ( -28.40)
>DroSim_CAF1 5752 120 - 1
GAAUUUUAAUUGCCACGUUUGCCAAAGUGUUUUGAUUGCUUUGUCAUUGCACUAAUCAGCACUUGUUCUCACUGCCUCACUUGGGGGCAUUUAUUAAUUAUAAAUUCCCUUCGAUGGCUC
...........((((((....(((((((((..((((......))))..))))).....(((..((....)).))).....))))(((.((((((.....)))))).)))..)).)))).. ( -28.40)
>DroEre_CAF1 6637 120 - 1
GAAUUUUAAUUGCCACGUUUGCCAAAGUGUUUUGAUUGCUUUGUCAUUGCACUAAUCAGCACUUGUUCUCACUGCCUCACUUGGGGGCAUUUAUUAAUUAUAAAUUCCCUUCGGUGGCUC
...........(((((.....(((((((((..((((......))))..))))).....(((..((....)).))).....))))(((.((((((.....)))))).)))....))))).. ( -30.80)
>DroYak_CAF1 6543 120 - 1
GAAUUUUAAUUGCCACGUUUGCCAAAGUGUUUUGAUUGCUUUGUCAUUGCACUAAUCAGCACUUGUUCUCACUGCCUCACUUGGGGGCAUUUAUUAAUUAUAAAUUCCCUUCGAUGGCUC
...........((((((....(((((((((..((((......))))..))))).....(((..((....)).))).....))))(((.((((((.....)))))).)))..)).)))).. ( -28.40)
>consensus
GAAUUUUAAUUGCCACGUUUGCCAAAGUGUUUUGAUUGCUUUGUCAUUGCACUAAUCAGCACUUGUUCUCACUGCCUCACUUGGGGGCAUUUAUUAAUUAUAAAUUCCCUUCGAUGGCUC
...........((((((....(((((((((..((((......))))..))))).....(((..((....)).))).....))))(((.((((((.....)))))).)))..)).)))).. (-28.40 = -28.40 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,143,309 – 19,143,428
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.50
Mean single sequence MFE -32.48
Consensus MFE -23.83
Energy contribution -23.03
Covariance contribution -0.80
Combinations/Pair 1.10
Mean z-score -2.33
Structure conservation index 0.73
SVM decision value 0.79
SVM RNA-class probability 0.852300
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19143309 119 - 23771897
AGAGCUCAGUGCAGUGCUCAGUGCUCAGUGGGCUU-UUGUGAAUUUUAAUUGCCACGUUUGCCAAAGUGUUUUGAUUGCUUUGUCAUUGCACUAAUCAGCACUUGUUCUCACUGCCUCAC
.(((..(((((.((.((..((((((.....(((..-.((((............))))...)))..(((((..((((......))))..)))))....)))))).)).))))))).))).. ( -37.00)
>DroSec_CAF1 6222 114 - 1
AGGGCUCA-----GUGCUCAGUGCUCAGUGGGCUU-UUGUGAAUUUUAAUUGCCACGUUUGCCAAAGUGUUUUGAUUGCUUUGUCAUUGCACUAAUCAGCACUUGUUCUCACUGCCUCAC
.((((..(-----(((..(((((((.....(((..-.((((............))))...)))..(((((..((((......))))..)))))....))))).))....))))))))... ( -32.50)
>DroSim_CAF1 5792 114 - 1
AGGGCUCA-----GUGCUCAGUGCUCAGUGGGCUU-UUGUGAAUUUUAAUUGCCACGUUUGCCAAAGUGUUUUGAUUGCUUUGUCAUUGCACUAAUCAGCACUUGUUCUCACUGCCUCAC
.((((..(-----(((..(((((((.....(((..-.((((............))))...)))..(((((..((((......))))..)))))....))))).))....))))))))... ( -32.50)
>DroEre_CAF1 6677 103 - 1
AGGGG----------------CUCUCAGUGGGCUU-UUGUGAAUUUUAAUUGCCACGUUUGCCAAAGUGUUUUGAUUGCUUUGUCAUUGCACUAAUCAGCACUUGUUCUCACUGCCUCAC
.((((----------------(....(((((((..-(((.......)))..)))(((..(((...(((((..((((......))))..))))).....)))..)))...))))))))).. ( -29.70)
>DroYak_CAF1 6583 109 - 1
AGGGG--------GUGG---UUUUUCAGUGGGCUUUUUGUGAAUUUUAAUUGCCACGUUUGCCAAAGUGUUUUGAUUGCUUUGUCAUUGCACUAAUCAGCACUUGUUCUCACUGCCUCAC
..(((--------(..(---(....((((((((....((((............))))...)))..(((((..((((......))))..)))))......))).)).....))..)))).. ( -30.70)
>consensus
AGGGCUCA_____GUGCUCAGUGCUCAGUGGGCUU_UUGUGAAUUUUAAUUGCCACGUUUGCCAAAGUGUUUUGAUUGCUUUGUCAUUGCACUAAUCAGCACUUGUUCUCACUGCCUCAC
.((((.................)))).((((((.....((((....(((.(((...(....)...(((((..((((......))))..))))).....))).)))...)))).))).))) (-23.83 = -23.03 +  -0.80)

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 12:37:18 2006