Locus 6690

Sequence ID 2L_DroMel_CAF1
Location 18,724,715 – 18,724,989
Length 274
Max. P 0.939052
window10675 window10676 window10677 window10678

overview

Window 5

Location 18,724,715 – 18,724,831
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.55
Mean single sequence MFE -30.18
Consensus MFE -24.70
Energy contribution -24.78
Covariance contribution 0.08
Combinations/Pair 1.13
Mean z-score -1.68
Structure conservation index 0.82
SVM decision value 0.59
SVM RNA-class probability 0.792268
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18724715 116 - 22407834
GAUGGCUUUGAUUGCGUUACACAUUUUGCUGGCUGCGAACGGAAUGUGCGCUGAUUUCAGCUGCCCUCUCUUUCUAGCCAGCUCAGGCCCUCUCUCUCUCUCUUUAUUUAUCUAU----C
((.(((((.((....(.....).....((((((((.(((.(((..(.((((((....)))).)).)..))))))))))))))))))))).)).......................----. ( -32.60)
>DroSec_CAF1 17323 102 - 1
GAUGGCUUUGAUUGCGUUACACAUUUUGCUGGCUGCGAACGGAAUGUGCGCUGAUUUCAGUUGCCCUCUCUUUCUGGCCAGCUCAGGCCCUCUCUCUC--------------UAU----C
((.(((((.((....(.....).....((((((((.(((.(((..(.((((((....))).))).)..))))))))))))))))))))).))......--------------...----. ( -29.40)
>DroSim_CAF1 15811 102 - 1
GAUGGCUUUGAUUGCGUUACACAUUUUGCUGGCUGCGAACGGAAUGUGCGCUGAUUUCAGUUGCCCUCUCUUUCUGGCCAGCUCAGGCCCUCUCUCUC--------------UAU----C
((.(((((.((....(.....).....((((((((.(((.(((..(.((((((....))).))).)..))))))))))))))))))))).))......--------------...----. ( -29.40)
>DroEre_CAF1 17483 102 - 1
GAUGGCUUUGAUUGCGUUACACAUUUUGCUGGCUGCGAACGGAAUGCGCGCUGAUUUUAGCUGCCCUCUCUUUCUGGCCAAGUCAGGCCCUCUCUCUC--------------GCU----C
((.(((((.(((((((..........)))((((((.(((.(((..(((.((((....)))))))..))).))).))))))))))))))).))......--------------...----. ( -27.80)
>DroYak_CAF1 17538 106 - 1
GAUGGCUUUGAUUGCGUUACACAUUUUGCUCGCUGCGAACGGAAUGUGCGCUGAUUUUAGAUGCCCUCUCUUUCUGGUCAUCUCAAGCCAUCUCUCUC--------------UGUAACAA
((((((((.((..(((...(((((((((.(((...))).))))))))))))........((((.((.........)).))))))))))))))......--------------........ ( -31.70)
>consensus
GAUGGCUUUGAUUGCGUUACACAUUUUGCUGGCUGCGAACGGAAUGUGCGCUGAUUUCAGCUGCCCUCUCUUUCUGGCCAGCUCAGGCCCUCUCUCUC______________UAU____C
((.(((((.((....(.....).....((((((((.(((.(((..(.((((((....))).))).)..))))))))))))))))))))).))............................ (-24.70 = -24.78 +   0.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,724,791 – 18,724,909
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.65
Mean single sequence MFE -40.90
Consensus MFE -39.80
Energy contribution -39.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.27
Structure conservation index 0.97
SVM decision value 0.39
SVM RNA-class probability 0.718346
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18724791 118 - 22407834
AUCGCAGGGGAGGAGGAGCUGGUUGCCCACUGGCAA--GAGCGUAAUCCAAGGUAGUUAAUUGCGCCUUAAACCGGAAGCGAUGGCUUUGAUUGCGUUACACAUUUUGCUGGCUGCGAAC
.((((((.......((.((.....)))).(..((((--((((((((((.(((((.....(((((.((.......))..))))).)))))))))))))......))))))..))))))).. ( -40.70)
>DroSec_CAF1 17385 118 - 1
AUCGCAGGGGAGGAGGAGCUGGUUGCCCACUGGCAA--GAGCGUAAUCCAAGGUAGUUAAUUGCGCCUUAAACCGGAAGCGAUGGCUUUGAUUGCGUUACACAUUUUGCUGGCUGCGAAC
.((((((.......((.((.....)))).(..((((--((((((((((.(((((.....(((((.((.......))..))))).)))))))))))))......))))))..))))))).. ( -40.70)
>DroSim_CAF1 15873 118 - 1
AUCGCAGGGGAGGAGGAGCUGGUUGCCCACUGGCAA--GAGCGUAAUCCAAGGUAGUUAAUUGCGCCUUAAACCGGAAGCGAUGGCUUUGAUUGCGUUACACAUUUUGCUGGCUGCGAAC
.((((((.......((.((.....)))).(..((((--((((((((((.(((((.....(((((.((.......))..))))).)))))))))))))......))))))..))))))).. ( -40.70)
>DroEre_CAF1 17545 120 - 1
AUCGCAGGGGAGGAGGAGCUGCUUGCCCACUGGCAACAGAGCGUAAUCCAAGGUAGUUAAUUGCGCCUUAAACCGGAAGCGAUGGCUUUGAUUGCGUUACACAUUUUGCUGGCUGCGAAC
.(((((((((..(((......))).))).(..((((...(((((((((.(((((.....(((((.((.......))..))))).)))))))))))))).......))))..))))))).. ( -41.60)
>DroYak_CAF1 17604 118 - 1
AUCGCAGGGGAGGAGGAGCUGGUUGCCCACUGGCAA--GAGCGUAAUCCAAGGUAGUUAAUUGCGCCUUAAACCGGAAGCGAUGGCUUUGAUUGCGUUACACAUUUUGCUCGCUGCGAAC
.((((((.(.((.((((..((.(((((....)))))--.(((((((((.(((((.....(((((.((.......))..))))).)))))))))))))).))..)))).))).)))))).. ( -40.80)
>consensus
AUCGCAGGGGAGGAGGAGCUGGUUGCCCACUGGCAA__GAGCGUAAUCCAAGGUAGUUAAUUGCGCCUUAAACCGGAAGCGAUGGCUUUGAUUGCGUUACACAUUUUGCUGGCUGCGAAC
.((((((.......((.((.....)))).(..((((...(((((((((.(((((.....(((((.((.......))..))))).)))))))))))))).......))))..))))))).. (-39.80 = -39.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,724,871 – 18,724,989
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.78
Mean single sequence MFE -44.71
Consensus MFE -39.06
Energy contribution -39.74
Covariance contribution 0.68
Combinations/Pair 1.08
Mean z-score -1.40
Structure conservation index 0.87
SVM decision value 0.63
SVM RNA-class probability 0.805018
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18724871 118 + 22407834
UC--UUGCCAGUGGGCAACCAGCUCCUCCUCCCCUGCGAUUCCCACUGCAAUUGGCGGUGGGAGCUUUGUAGUGGCGGUUCGGACUGGGGACCCGGCUUUGCUAUAUAUAGCGUCAUGGC
..--..((((..(((...((((.(((.((.((.((((((((((((((((.....))))))))))..)))))).)).))...)))))))...)))(((...((((....))))))).)))) ( -53.30)
>DroSec_CAF1 17465 118 + 1
UC--UUGCCAGUGGGCAACCAGCUCCUCCUCCCCUGCGAUUCCCACUGCAUUUGGCGGUGGAAGCUUUGUAGUGCCCGUUCGGACUGGGGACCCGACUUUGCUAUAUUUAGCGUCAUGGC
..--..((((..(((...((((.(((......(((((((...(((((((.....))))))).....)))))).).......)))))))...)))(((...((((....))))))).)))) ( -41.02)
>DroSim_CAF1 15953 118 + 1
UC--UUGCCAGUGGGCAACCAGCUCCUCCUCCCCUGCGAUUCCCACUGCAAUUGGCGGUGGGAGCUUUGUAGUGCCCGUUCGGACUGGGGACCCGACUUUGCUAUAUAUAGCGUCAUGGC
..--..((((..(((...((((.(((......(((((((((((((((((.....))))))))))..)))))).).......)))))))...)))(((...((((....))))))).)))) ( -46.02)
>DroEre_CAF1 17625 118 + 1
UCUGUUGCCAGUGGGCAAGCAGCUCCUCCUCCCCUGCGAUUCCCACUGCAAUUGGCGGUGGGAGCUUUGUAGUGCCCGUUCGGACGG-GGACCCGAUUUU-CUAUAUAUAGCGUCAUGGC
......((((...(((..((((...........))))...(((((((((.....)))))))))(((.((((((.(((((....))))-).))..(.....-)..)))).)))))).)))) ( -42.60)
>DroYak_CAF1 17684 117 + 1
UC--UUGCCAGUGGGCAACCAGCUCCUCCUCCCCUGCGAUUUCCACUGCAAUUGGCGGUGGGAGCUUUGUAGUGCCCGUUCGGACGGGGGACCCGAUUUU-CUAUAUAUAGCGUCAUGGC
..--..((((.(((....)))(((((((((((...(((..(((((((((.....)))))))))((........)).)))..))).))))))...(.....-)........))....)))) ( -40.60)
>consensus
UC__UUGCCAGUGGGCAACCAGCUCCUCCUCCCCUGCGAUUCCCACUGCAAUUGGCGGUGGGAGCUUUGUAGUGCCCGUUCGGACUGGGGACCCGACUUUGCUAUAUAUAGCGUCAUGGC
......((((..(((...((((.(((......(((((((((((((((((.....))))))))))..)))))).).......)))))))...)))(((...((((....))))))).)))) (-39.06 = -39.74 +   0.68)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,724,871 – 18,724,989
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.78
Mean single sequence MFE -43.22
Consensus MFE -37.54
Energy contribution -38.38
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -1.65
Structure conservation index 0.87
SVM decision value 1.30
SVM RNA-class probability 0.939052
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18724871 118 - 22407834
GCCAUGACGCUAUAUAUAGCAAAGCCGGGUCCCCAGUCCGAACCGCCACUACAAAGCUCCCACCGCCAAUUGCAGUGGGAAUCGCAGGGGAGGAGGAGCUGGUUGCCCACUGGCAA--GA
((((....((((....))))......((((..(((((((...((.((.((.......((((((.((.....)).))))))......)))).)).))).))))..))))..))))..--.. ( -45.22)
>DroSec_CAF1 17465 118 - 1
GCCAUGACGCUAAAUAUAGCAAAGUCGGGUCCCCAGUCCGAACGGGCACUACAAAGCUUCCACCGCCAAAUGCAGUGGGAAUCGCAGGGGAGGAGGAGCUGGUUGCCCACUGGCAA--GA
((((.(((((((....))))...)))((((..((.((((....)))).......((((.((.((.((...(((.((....)).)))..)).)).))))))))..))))..))))..--.. ( -44.30)
>DroSim_CAF1 15953 118 - 1
GCCAUGACGCUAUAUAUAGCAAAGUCGGGUCCCCAGUCCGAACGGGCACUACAAAGCUCCCACCGCCAAUUGCAGUGGGAAUCGCAGGGGAGGAGGAGCUGGUUGCCCACUGGCAA--GA
((((.(((((((....))))...)))((((..((.((((....)))).......((((((..((.((..((((.((....)).)))).)).)).))))))))..))))..))))..--.. ( -45.30)
>DroEre_CAF1 17625 118 - 1
GCCAUGACGCUAUAUAUAG-AAAAUCGGGUCC-CCGUCCGAACGGGCACUACAAAGCUCCCACCGCCAAUUGCAGUGGGAAUCGCAGGGGAGGAGGAGCUGCUUGCCCACUGGCAACAGA
.((.(((..(((....)))-....)))..(((-((((((....))))........((((((((.((.....)).))))))...)).))))))).((.((.....)))).(((....))). ( -40.30)
>DroYak_CAF1 17684 117 - 1
GCCAUGACGCUAUAUAUAG-AAAAUCGGGUCCCCCGUCCGAACGGGCACUACAAAGCUCCCACCGCCAAUUGCAGUGGAAAUCGCAGGGGAGGAGGAGCUGGUUGCCCACUGGCAA--GA
((((.((..(((....)))-....))((((..((.((((....)))).......((((((..((.((..((((.((....)).)))).)).)).))))))))..))))..))))..--.. ( -41.00)
>consensus
GCCAUGACGCUAUAUAUAGCAAAGUCGGGUCCCCAGUCCGAACGGGCACUACAAAGCUCCCACCGCCAAUUGCAGUGGGAAUCGCAGGGGAGGAGGAGCUGGUUGCCCACUGGCAA__GA
((((....((((....))))......((((..((.((((....)))).......((((((..((.((...(((.((....)).)))..)).)).))))))))..))))..))))...... (-37.54 = -38.38 +   0.84)

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 12:17:33 2006