Locus 6461

Sequence ID 3L_DroMel_CAF1
Location 17,236,856 – 17,237,051
Length 195
Max. P 0.988753
window10391 window10392 window10393 window10394

overview

Window 1

Location 17,236,856 – 17,236,976
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.55
Mean single sequence MFE -38.01
Consensus MFE -32.82
Energy contribution -32.42
Covariance contribution -0.40
Combinations/Pair 1.07
Mean z-score -1.40
Structure conservation index 0.86
SVM decision value 0.58
SVM RNA-class probability 0.789463
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17236856 120 + 23771897
CUCAGUUGGGUUUGCCAUUAGCAUUCGCAAUGGGUUUUCGCAUACCAAUGCCCAUGUGCACUUACGAGUAGAAAAGGGCUUUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAA
(((.((.(((..(((.....)))..)(((((((((..............)))))).))).)).)))))........((((...((((((((....))))))))......))))....... ( -36.94)
>DroSec_CAF1 120849 120 + 1
CUCAGUUGGGCUUGCCAUUAGCAUUCGCAAUGGGUUUUCGCAUACCAAUGCCCAUGUGCACUUACGAGUGGAAAAGGGCUUUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAA
.....((((.....(((((.((....)))))))...........(((((((((...(.((((....)))).)...))))....((((((((....))))))))...)))))))))..... ( -40.00)
>DroSim_CAF1 114694 120 + 1
CUCAGUUGGGCUUGCCAUUAGCAUUCGCAAUGGGUUUUCGCAUACCAAUGCCCAUGUGCACUUACGAGUGGAAAAGGGCUUUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAA
.....((((.....(((((.((....)))))))...........(((((((((...(.((((....)))).)...))))....((((((((....))))))))...)))))))))..... ( -40.00)
>DroEre_CAF1 124165 113 + 1
CUCAGUGGGGCUGGCCAUUAGCAU-UGCAAUGGAUUUUCGCAUACCAAUGCCCAUGUGCACUUA------GAAAAGGGCUUUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCUAAGACAA
..(((.....)))(((((..((((-((..((((.....).)))..))))))..))).)).((((------(.....((((...((((((((....))))))))..))))..))))).... ( -34.60)
>DroYak_CAF1 127235 114 + 1
CUCAGUUGGGUUUGCCAUUAGCAUUUGCAAUGGCUUUCCGCAUACCAAUGCCCAUGUGCACUUA------GAAAAGGGCUUUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAA
....((((((...((((((.((....))))))))..))).....(((((((((...........------.....))))....((((((((....))))))))...)))))....))).. ( -38.49)
>consensus
CUCAGUUGGGCUUGCCAUUAGCAUUCGCAAUGGGUUUUCGCAUACCAAUGCCCAUGUGCACUUACGAGU_GAAAAGGGCUUUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAA
....((..((((.(((....((((..(((.(((...........))).)))....)))).(((..........))))))....((((((((....))))))))......))))...)).. (-32.82 = -32.42 +  -0.40)

alignment

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secondary structure

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Window 2

Location 17,236,856 – 17,236,976
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.55
Mean single sequence MFE -32.86
Consensus MFE -29.69
Energy contribution -29.33
Covariance contribution -0.36
Combinations/Pair 1.10
Mean z-score -1.17
Structure conservation index 0.90
SVM decision value 0.21
SVM RNA-class probability 0.635907
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17236856 120 - 23771897
UUGUCUUGGCCAACUGACAGCCUACUUUCGCAAGCCGAAAAGCCCUUUUCUACUCGUAAGUGCACAUGGGCAUUGGUAUGCGAAAACCCAUUGCGAAUGCUAAUGGCAAACCCAACUGAG
((((((((((....((.(((.....(((((((.(((((...((((.....((((....)))).....)))).))))).))))))).....)))))...))))).)))))........... ( -32.30)
>DroSec_CAF1 120849 120 - 1
UUGUCUUGGCCAACUGACAGCCUACUUUCGCAAGCCGAAAAGCCCUUUUCCACUCGUAAGUGCACAUGGGCAUUGGUAUGCGAAAACCCAUUGCGAAUGCUAAUGGCAAGCCCAACUGAG
.......(((...............(((((((.(((((...((((.....((((....)))).....)))).))))).)))))))..(((((((....)).)))))...)))........ ( -34.30)
>DroSim_CAF1 114694 120 - 1
UUGUCUUGGCCAACUGACAGCCUACUUUCGCAAGCCGAAAAGCCCUUUUCCACUCGUAAGUGCACAUGGGCAUUGGUAUGCGAAAACCCAUUGCGAAUGCUAAUGGCAAGCCCAACUGAG
.......(((...............(((((((.(((((...((((.....((((....)))).....)))).))))).)))))))..(((((((....)).)))))...)))........ ( -34.30)
>DroEre_CAF1 124165 113 - 1
UUGUCUUAGCCAACUGACAGCCUACUUUCGCAAGCCGAAAAGCCCUUUUC------UAAGUGCACAUGGGCAUUGGUAUGCGAAAAUCCAUUGCA-AUGCUAAUGGCCAGCCCCACUGAG
....(((((....(((.........(((((((.(((((...((((.....------...........)))).))))).)))))))..(((((((.-..)).))))).))).....))))) ( -29.49)
>DroYak_CAF1 127235 114 - 1
UUGUCUUGGCCAACUGACAGCCUACUUUCGCAAGCCGAAAAGCCCUUUUC------UAAGUGCACAUGGGCAUUGGUAUGCGGAAAGCCAUUGCAAAUGCUAAUGGCAAACCCAACUGAG
(((((..(.....).))))).....(((((((.(((((...((((.....------...........)))).))))).))))))).((((((((....)).))))))............. ( -33.89)
>consensus
UUGUCUUGGCCAACUGACAGCCUACUUUCGCAAGCCGAAAAGCCCUUUUC_ACUCGUAAGUGCACAUGGGCAUUGGUAUGCGAAAACCCAUUGCGAAUGCUAAUGGCAAGCCCAACUGAG
((((((((((....((.(((.....(((((((.(((((...((((......................)))).))))).))))))).....)))))...))))).)))))........... (-29.69 = -29.33 +  -0.36)

alignment

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secondary structure

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Window 3

Location 17,236,896 – 17,237,013
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.54
Mean single sequence MFE -38.88
Consensus MFE -33.51
Energy contribution -33.35
Covariance contribution -0.16
Combinations/Pair 1.10
Mean z-score -1.98
Structure conservation index 0.86
SVM decision value 2.13
SVM RNA-class probability 0.988753
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17236896 117 + 23771897
CAUACCAAUGCCCAUGUGCACUUACGAGUAGAAAAGGGCUUUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAAAUGGCCGGAGCUUGGCUAAGAAGA---UGAUGAAGGGGAG
..........(((.....(((((...(((......(((((((.((((((((....))))))))......(((((.......)))))))))))).)))...))).---))......))).. ( -36.80)
>DroSec_CAF1 120889 117 + 1
CAUACCAAUGCCCAUGUGCACUUACGAGUGGAAAAGGGCUUUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAAAUGGCCGGAGCUUGGCUAAGACGA---UGAUGAAGGGGAG
....((...((((...(.((((....)))).)...))))((((((((((((....)))))))(((..(((((((((.(........)...))))))))))))..---....))))))).. ( -41.80)
>DroSim_CAF1 114734 117 + 1
CAUACCAAUGCCCAUGUGCACUUACGAGUGGAAAAGGGCUUUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAAAUGGCCGGAGCUUGGCUAAGACGA---UGAUGAAGGGGAG
....((...((((...(.((((....)))).)...))))((((((((((((....)))))))(((..(((((((((.(........)...))))))))))))..---....))))))).. ( -41.80)
>DroEre_CAF1 124204 111 + 1
CAUACCAAUGCCCAUGUGCACUUA------GAAAAGGGCUUUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCUAAGACAAAUGGCCGCAGCUUGGCUAAGACGA---UGAUGCAGAGGAG
....((..(((.(((((...((((------(..(((((((...((((((((....))))))))..))))(((((.......)))))....)))..))))))).)---))..)))..)).. ( -36.00)
>DroYak_CAF1 127275 114 + 1
CAUACCAAUGCCCAUGUGCACUUA------GAAAAGGGCUUUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAAAUGGCCGGAGCUUGGCUAAGACGAGGAUGAUGAGGAGGAG
(((.((..(((......)))((((------(....(((((((.((((((((....))))))))......(((((.......))))))))))))..)))))....)))))........... ( -38.00)
>consensus
CAUACCAAUGCCCAUGUGCACUUACGAGU_GAAAAGGGCUUUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAAAUGGCCGGAGCUUGGCUAAGACGA___UGAUGAAGGGGAG
....((...((((......................))))((((((((((((....)))))))(((..(((((((((.(........)...)))))))))))).........))))))).. (-33.51 = -33.35 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,236,936 – 17,237,051
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.38
Mean single sequence MFE -38.06
Consensus MFE -35.90
Energy contribution -36.14
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.11
Structure conservation index 0.94
SVM decision value 0.21
SVM RNA-class probability 0.633467
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17236936 115 + 23771897
UUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAAAUGGCCGGAGCUUGGCUAAGAAGA---UGAUGAAGGGGAGAAGCCGUUAACACA--UGCUCAGACGCGACGAGUGACGGG
(((((((((((....)))))))((((.(((((((((.(........)...))))))))).....---))))......))))..((((((.....--(((......))).....)))))). ( -36.40)
>DroSec_CAF1 120929 115 + 1
UUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAAAUGGCCGGAGCUUGGCUAAGACGA---UGAUGAAGGGGAGAAGCCGUUAACACA--UGCUCAGACGCGACGACUGACGGG
....(((((((....)))))))((((((((((((.......))))).((((..((((....(..---(.....)..)....))))((....)).--.)))).........)))))))... ( -38.70)
>DroSim_CAF1 114774 115 + 1
UUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAAAUGGCCGGAGCUUGGCUAAGACGA---UGAUGAAGGGGAGAAGCCGUUAACACA--UGCUCAGACGCGACGACUGACGGG
....(((((((....)))))))((((((((((((.......))))).((((..((((....(..---(.....)..)....))))((....)).--.)))).........)))))))... ( -38.70)
>DroEre_CAF1 124238 115 + 1
UUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCUAAGACAAAUGGCCGCAGCUUGGCUAAGACGA---UGAUGCAGAGGAGGAGCCGUUAACACA--UGCUCAGACGCGACGACUGACGGG
....(((((((....)))))))((((((((((((.......))))(((..(((.((........---....)).)))...((((.((....)).--.))))....))).))))))))... ( -37.30)
>DroYak_CAF1 127309 120 + 1
UUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAAAUGGCCGGAGCUUGGCUAAGACGAGGAUGAUGAGGAGGAGAAGCCGUUAACACAUAUGCUCAGACGCGACGACUGACGGG
....(((((((....)))))))((((((((((((((.(........)...))))))......(((.(((.((.(..((.....)).....).))))).)))........))))))))... ( -39.20)
>consensus
UUUCGGCUUGCGAAAGUAGGCUGUCAGUUGGCCAAGACAAAUGGCCGGAGCUUGGCUAAGACGA___UGAUGAAGGGGAGAAGCCGUUAACACA__UGCUCAGACGCGACGACUGACGGG
....(((((((....)))))))((((((((((((.......))))).((((..((((........................))))((....))....)))).........)))))))... (-35.90 = -36.14 +   0.24)

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 12:19:47 2006