Locus 4530

Sequence ID X_DroMel_CAF1
Location 11,940,475 – 11,940,608
Length 133
Max. P 0.950657
window7446 window7447 window7448 window7449

overview

Window 6

Location 11,940,475 – 11,940,571
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 89.23
Mean single sequence MFE -35.53
Consensus MFE -30.49
Energy contribution -30.35
Covariance contribution -0.14
Combinations/Pair 1.03
Mean z-score -2.00
Structure conservation index 0.86
SVM decision value 0.82
SVM RNA-class probability 0.858403
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11940475 96 + 22224390
GG------------------------AGCAGCAGCUUGCCUCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUUGGCGGA
.(------------------------(((((((((.((((..(((.......))))))).))))).(((((.....)))))...((((((((((....)))))))))).)))))...... ( -34.60)
>DroVir_CAF1 28913 96 + 1
GG------------------------CGCGCCAGCUUGCCUCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUUGGCGGA
..------------------------..(((((((.((((..(((.......)))))))....)).(((((.....)))))...((((((((((....)))))))))).....))))).. ( -33.50)
>DroGri_CAF1 4755 96 + 1
GG------------------------CGCGCCAGCUUGCCUCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUUGGCGGA
..------------------------..(((((((.((((..(((.......)))))))....)).(((((.....)))))...((((((((((....)))))))))).....))))).. ( -33.50)
>DroYak_CAF1 7872 96 + 1
GG------------------------AGCAGCAGCUUGCCUCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUUGGCGGA
.(------------------------(((((((((.((((..(((.......))))))).))))).(((((.....)))))...((((((((((....)))))))))).)))))...... ( -34.60)
>DroAna_CAF1 3198 120 + 1
GGCGUGACAGCGAUGGCGACGAGGACGGCGACGGCUUGCCUCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUGAGCGGA
((((((((.((((((((...((((..(((....)))..))))(((.......))).)).)))))).))))))))...(((((..((((((((((....)))))))))).)))))...... ( -44.40)
>DroMoj_CAF1 3826 96 + 1
GG------------------------CGCGCCAGCUUGCCUCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUUAGCGGA
((------------------------(.(((.(((.((((..(((.......))))))).))))))))).(((((((((.....((((((((((....)))))))))).))))))))).. ( -32.60)
>consensus
GG________________________CGCGCCAGCUUGCCUCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUUGGCGGA
...........................((..((((.((((..(((.......))))))).))))(.(((((.....))))).).((((((((((....)))))))))).......))... (-30.49 = -30.35 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,940,475 – 11,940,571
Length 96
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 89.23
Mean single sequence MFE -26.02
Consensus MFE -22.95
Energy contribution -22.73
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.77
Structure conservation index 0.88
SVM decision value 0.83
SVM RNA-class probability 0.862016
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11940475 96 - 22224390
UCCGCCAAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGAGGCAAGCUGCUGCU------------------------CC
...(((.......((((((((......)))))))).((((((((.....))))).((.....)).)))............))).(((....)))------------------------.. ( -24.60)
>DroVir_CAF1 28913 96 - 1
UCCGCCAAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGAGGCAAGCUGGCGCG------------------------CC
..(((((......((((((((......))))))))....(((((.....))))).((....(((((((.......)))..)))).)))))))..------------------------.. ( -26.90)
>DroGri_CAF1 4755 96 - 1
UCCGCCAAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGAGGCAAGCUGGCGCG------------------------CC
..(((((......((((((((......))))))))....(((((.....))))).((....(((((((.......)))..)))).)))))))..------------------------.. ( -26.90)
>DroYak_CAF1 7872 96 - 1
UCCGCCAAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGAGGCAAGCUGCUGCU------------------------CC
...(((.......((((((((......)))))))).((((((((.....))))).((.....)).)))............))).(((....)))------------------------.. ( -24.60)
>DroAna_CAF1 3198 120 - 1
UCCGCUCAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGAGGCAAGCCGUCGCCGUCCUCGUCGCCAUCGCUGUCACGCC
................((.....(((((((((....((((((((.....))))).((.....)).))).........(((((...((....))...)))))..).))))))))....)). ( -28.30)
>DroMoj_CAF1 3826 96 - 1
UCCGCUAAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGAGGCAAGCUGGCGCG------------------------CC
..(((........((((((((......))))))))....(((((.....))))).((..(.(((((((.......)))..)))).)...)))))------------------------.. ( -24.80)
>consensus
UCCGCCAAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGAGGCAAGCUGGCGCG________________________CC
...(((.......((((((((......)))))))).((((((((.....))))).((.....)).)))............)))..((....))........................... (-22.95 = -22.73 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,940,491 – 11,940,608
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.11
Mean single sequence MFE -40.67
Consensus MFE -34.33
Energy contribution -34.83
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.47
Structure conservation index 0.84
SVM decision value 1.25
SVM RNA-class probability 0.935550
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11940491 117 + 22224390
UCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUUGGCGGAAAUGAAAGCGGUUUCGUGUGACGACUUGGCGCGC---UUA
(((..(((((((((((.((...(((.(((((.....)))))...((((((((((....)))))))))))))..)).))))))))))).)))....(((((.(......))))))---... ( -41.70)
>DroVir_CAF1 28929 119 + 1
UCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUUGGCGGAAAUGAAAGCGGUUUCGUGUGACGACUUGCCAGCCCAC-AC
..((.(((((((((((.((...(((.(((((.....)))))...((((((((((....)))))))))))))..)).)))))))))))(((((.(((.....)))...))).))))..-.. ( -43.40)
>DroGri_CAF1 4771 120 + 1
UCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUUGGCGGAAAUGAAAGCGGUUUCAUGUGACGACUUGCCAGCCCUCUAA
..((.(((((((((((.((...(((.(((((.....)))))...((((((((((....)))))))))))))..)).)))))))))))(((((.((.......))...))).))))..... ( -39.80)
>DroYak_CAF1 7888 117 + 1
UCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUUGGCGGAAAUGAAAGCGGUUUCGUGUGACGACUUGACGCGC---UUA
.......(((((((((.((...(((.(((((.....)))))...((((((((((....)))))))))))))..)).)))))))))(((((((((((.....)))...))).)))---)). ( -42.10)
>DroAna_CAF1 3238 113 + 1
UCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUGAGCGGAAAUGAAAGCGGGCACACCUU----CUGGAGAGGC---ACA
(((..(((((((((((((((....(.(((((.....))))).).((((((((((....))))))))))))))....))))))))))).)))((.(.((..----..)).)..))---... ( -37.60)
>DroMoj_CAF1 3842 119 + 1
UCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUUAGCGGAAAUGAAAGCGGUUUCGUGUGACGCCUUGCCAGCCCAC-AA
..((.(((((((((((((((....(.(((((.....))))).).((((((((((....))))))))))))))....)))))))))))(((((...(((...)))...))).))))..-.. ( -39.40)
>consensus
UCGGAUUUCAUUUCCGGCAUGUUGCGGUUACGUUAAGUAACGGAGAUUGCAUCGCUAAUGAUGCAAUUGUGUUUGGCGGAAAUGAAAGCGGUUUCGUGUGACGACUUGCCAGCC___UAA
(((..(((((((((((.((...(((.(((((.....)))))...((((((((((....)))))))))))))..)).))))))))))).)))............................. (-34.33 = -34.83 +   0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 11,940,491 – 11,940,608
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.11
Mean single sequence MFE -34.57
Consensus MFE -27.81
Energy contribution -27.75
Covariance contribution -0.06
Combinations/Pair 1.04
Mean z-score -3.34
Structure conservation index 0.80
SVM decision value 1.40
SVM RNA-class probability 0.950657
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11940491 117 - 22224390
UAA---GCGCGCCAAGUCGUCACACGAAACCGCUUUCAUUUCCGCCAAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGA
...---..(((.....(((.....)))...)))(((((((((((.((......((((((((......))))))))....(((((.....))))).......)).)))))))))))..... ( -33.30)
>DroVir_CAF1 28929 119 - 1
GU-GUGGGCUGGCAAGUCGUCACACGAAACCGCUUUCAUUUCCGCCAAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGA
((-(((((((....))))..))))).....((.(((((((((((.((......((((((((......))))))))....(((((.....))))).......)).)))))))))))..)). ( -38.10)
>DroGri_CAF1 4771 120 - 1
UUAGAGGGCUGGCAAGUCGUCACAUGAAACCGCUUUCAUUUCCGCCAAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGA
...((.((((....)))).)).........((.(((((((((((.((......((((((((......))))))))....(((((.....))))).......)).)))))))))))..)). ( -35.90)
>DroYak_CAF1 7888 117 - 1
UAA---GCGCGUCAAGUCGUCACACGAAACCGCUUUCAUUUCCGCCAAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGA
..(---(((.((....(((.....))).))))))((((((((((.((......((((((((......))))))))....(((((.....))))).......)).))))))))))...... ( -34.20)
>DroAna_CAF1 3238 113 - 1
UGU---GCCUCUCCAG----AAGGUGUGCCCGCUUUCAUUUCCGCUCAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGA
.(.---.((((....)----.)))..)...((.(((((((((((.........((((((((......))))))))....(((((.....))))).((.....)))))))))))))..)). ( -31.40)
>DroMoj_CAF1 3842 119 - 1
UU-GUGGGCUGGCAAGGCGUCACACGAAACCGCUUUCAUUUCCGCUAAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGA
.(-(((((((.....))).)))))......((.(((((((((((.........((((((((......))))))))....(((((.....))))).((.....)))))))))))))..)). ( -34.50)
>consensus
UUA___GCCUGGCAAGUCGUCACACGAAACCGCUUUCAUUUCCGCCAAACACAAUUGCAUCAUUAGCGAUGCAAUCUCCGUUACUUAACGUAACCGCAACAUGCCGGAAAUGAAAUCCGA
..............................((.(((((((((((.((......((((((((......))))))))....(((((.....))))).......)).)))))))))))..)). (-27.81 = -27.75 +  -0.06)

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 11:27:24 2006