Locus 3052

Sequence ID 2R_DroMel_CAF1
Location 10,514,120 – 10,514,279
Length 159
Max. P 0.999887
window5025 window5026 window5027 window5028

overview

Window 5

Location 10,514,120 – 10,514,239
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.99
Mean single sequence MFE -22.52
Consensus MFE -19.98
Energy contribution -20.78
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 0.89
SVM decision value 1.27
SVM RNA-class probability 0.938340
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10514120 119 + 20766785
CAAACAUUUUACGGUUUCACCUCGAAAUUAAAUUUCCCCU-UUCAAUACCGACCAAAAAAGCCGCAUCGAUAGACGGCCAAAACGUGGCAUCAUGGUGAAAACUAAAAUCAAAUUGCCAC
...........((((........(((((...)))))....-......)))).........((((..((....))))))......((((((...((((..........))))...)))))) ( -20.87)
>DroSec_CAF1 14706 120 + 1
CAAACAUUUUACGGUUUCACCUCGAAAUUAAAUUUCCCCUUUUCAAUACCGGCCAAAAAAGCCGCAUCGAUAGACGGCCAAAACGUGGCAUCAUGGUGAAAACUAAAAUCAAAUUGCUAC
.....((((((...(((((((..((((.............)))).......((((.....((((..((....)))))).......)))).....)))))))..))))))........... ( -23.32)
>DroSim_CAF1 9727 120 + 1
CAAACAUUUUACGGUUUCACCUCGAAAUUAAAUUUCCCCUUUUCAAUACCGGCCAAAAAAGCCGCAUCGAUAGACGGCCAAAACGUGGCAUCAUGGUGAAAACUAAAAUCAAAUUGCCAC
.....((((((...(((((((..((((.............)))).......((((.....((((..((....)))))).......)))).....)))))))..))))))........... ( -23.32)
>DroEre_CAF1 14852 119 + 1
CAAACACUUUACGGUCUCACCUCGAAAUUAAAUUUCCCCU-UUCAAUGCCCGCCAAAAAAGCCGCAUCGAUAGACGGCCAAAACGUGGCAUCAUGGUGAAAACUAAAAUCAAAUUGCCAC
............((((.......(((((...)))))..((-.((.((((..((.......)).)))).)).))..)))).....((((((...((((..........))))...)))))) ( -22.90)
>DroYak_CAF1 11418 118 + 1
CAAACACUUUACGGUUUCACCUCGAAAUUAAAUUUCCCCU-UUCAAUAUCGGCCAA-AAAGCCGCAUCGAUAGACGGCCCGAACGUGGCAUCAUGGUGAAAACUAAAAUCAAAUUGCCAC
............(((((((((.(((.(((.((........-)).))).)))((((.-...((((..((....)))))).......)))).....)))).)))))................ ( -22.20)
>consensus
CAAACAUUUUACGGUUUCACCUCGAAAUUAAAUUUCCCCU_UUCAAUACCGGCCAAAAAAGCCGCAUCGAUAGACGGCCAAAACGUGGCAUCAUGGUGAAAACUAAAAUCAAAUUGCCAC
.....((((((...(((((((..(((((...)))))...............((((.....((((..((....)))))).......)))).....)))))))..))))))........... (-19.98 = -20.78 +   0.80)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,514,120 – 10,514,239
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.99
Mean single sequence MFE -32.70
Consensus MFE -31.10
Energy contribution -31.18
Covariance contribution 0.08
Combinations/Pair 1.05
Mean z-score -1.18
Structure conservation index 0.95
SVM decision value 0.47
SVM RNA-class probability 0.747205
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10514120 119 - 20766785
GUGGCAAUUUGAUUUUAGUUUUCACCAUGAUGCCACGUUUUGGCCGUCUAUCGAUGCGGCUUUUUUGGUCGGUAUUGAA-AGGGGAAAUUUAAUUUCGAGGUGAAACCGUAAAAUGUUUG
...........(((((((.(((((((.(((.((((.....))))(.(((.(((((((((((.....)))).))))))).-))).)..........))).))))))).).))))))..... ( -31.20)
>DroSec_CAF1 14706 120 - 1
GUAGCAAUUUGAUUUUAGUUUUCACCAUGAUGCCACGUUUUGGCCGUCUAUCGAUGCGGCUUUUUUGGCCGGUAUUGAAAAGGGGAAAUUUAAUUUCGAGGUGAAACCGUAAAAUGUUUG
((..((.(((((..((((.((((.((..(((((((.....))).))))..(((((((((((.....)))).)))))))...)).)))).))))..))))).))..))............. ( -32.20)
>DroSim_CAF1 9727 120 - 1
GUGGCAAUUUGAUUUUAGUUUUCACCAUGAUGCCACGUUUUGGCCGUCUAUCGAUGCGGCUUUUUUGGCCGGUAUUGAAAAGGGGAAAUUUAAUUUCGAGGUGAAACCGUAAAAUGUUUG
((..((.(((((..((((.((((.((..(((((((.....))).))))..(((((((((((.....)))).)))))))...)).)))).))))..))))).))..))............. ( -33.20)
>DroEre_CAF1 14852 119 - 1
GUGGCAAUUUGAUUUUAGUUUUCACCAUGAUGCCACGUUUUGGCCGUCUAUCGAUGCGGCUUUUUUGGCGGGCAUUGAA-AGGGGAAAUUUAAUUUCGAGGUGAGACCGUAAAGUGUUUG
((..((.(((((..((((.((((.((.(((((((.((((..((((((........)))))).....)))))))))))..-..)))))).))))..))))).))..))............. ( -33.80)
>DroYak_CAF1 11418 118 - 1
GUGGCAAUUUGAUUUUAGUUUUCACCAUGAUGCCACGUUCGGGCCGUCUAUCGAUGCGGCUUU-UUGGCCGAUAUUGAA-AGGGGAAAUUUAAUUUCGAGGUGAAACCGUAAAGUGUUUG
...........(((((((.(((((((.(((.(((.(....))))(.(((.(((((((((((..-..))))).)))))).-))).)..........))).))))))).).))))))..... ( -33.10)
>consensus
GUGGCAAUUUGAUUUUAGUUUUCACCAUGAUGCCACGUUUUGGCCGUCUAUCGAUGCGGCUUUUUUGGCCGGUAUUGAA_AGGGGAAAUUUAAUUUCGAGGUGAAACCGUAAAAUGUUUG
((..((.(((((..((((.((((.((..(((((((.....))).))))..(((((((((((.....))))).))))))...)).)))).))))..))))).))..))............. (-31.10 = -31.18 +   0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,514,160 – 10,514,279
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.82
Mean single sequence MFE -34.74
Consensus MFE -31.22
Energy contribution -32.06
Covariance contribution 0.84
Combinations/Pair 1.03
Mean z-score -3.75
Structure conservation index 0.90
SVM decision value 4.39
SVM RNA-class probability 0.999887
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10514160 119 + 20766785
-UUCAAUACCGACCAAAAAAGCCGCAUCGAUAGACGGCCAAAACGUGGCAUCAUGGUGAAAACUAAAAUCAAAUUGCCACGGCCAGCCAUGAAAAUCGUAGAAAUUAUCAGAUGCCAAAG
-......................((((((((((..(((.....(((((((...((((..........))))...)))))))....)))(((.....))).....))))).)))))..... ( -29.50)
>DroSec_CAF1 14746 120 + 1
UUUCAAUACCGGCCAAAAAAGCCGCAUCGAUAGACGGCCAAAACGUGGCAUCAUGGUGAAAACUAAAAUCAAAUUGCUACGGCCAGCCAUGAAAAUCGUGGAAAUUAUCAGAUGCCAAAG
..........(((.......)))((((((((((..((((.....((((((...((((..........))))...))))))))))..(((((.....)))))...))))).)))))..... ( -35.90)
>DroSim_CAF1 9767 120 + 1
UUUCAAUACCGGCCAAAAAAGCCGCAUCGAUAGACGGCCAAAACGUGGCAUCAUGGUGAAAACUAAAAUCAAAUUGCCACGGCCAGCCAUGAAAAUCGUGGAAAUUAUCAGAUGCCAAAG
..........(((.......)))((((((((((..((((.....((((((...((((..........))))...))))))))))..(((((.....)))))...))))).)))))..... ( -38.20)
>DroEre_CAF1 14892 119 + 1
-UUCAAUGCCCGCCAAAAAAGCCGCAUCGAUAGACGGCCAAAACGUGGCAUCAUGGUGAAAACUAAAAUCAAAUUGCCACGGCCAGCCAUGAAAAUCGUGAAAAUUAUCAGAUGCCAAAG
-......................((((((((((..((((.....((((((...((((..........))))...))))))))))...((((.....))))....))))).)))))..... ( -31.20)
>DroYak_CAF1 11458 118 + 1
-UUCAAUAUCGGCCAA-AAAGCCGCAUCGAUAGACGGCCCGAACGUGGCAUCAUGGUGAAAACUAAAAUCAAAUUGCCACGGCCAGCGAUGAAAAUCGUGGAAAUUAUCAGAUGCCAAAG
-.........(((...-...)))((((((((((..((((.....((((((...((((..........))))...)))))))))).(((((....))))).....))))).)))))..... ( -38.90)
>consensus
_UUCAAUACCGGCCAAAAAAGCCGCAUCGAUAGACGGCCAAAACGUGGCAUCAUGGUGAAAACUAAAAUCAAAUUGCCACGGCCAGCCAUGAAAAUCGUGGAAAUUAUCAGAUGCCAAAG
..........(((.......)))((((((((((..((((.....((((((...((((..........))))...))))))))))..(((((.....)))))...))))).)))))..... (-31.22 = -32.06 +   0.84)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,514,160 – 10,514,279
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.82
Mean single sequence MFE -33.26
Consensus MFE -30.96
Energy contribution -31.08
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -1.61
Structure conservation index 0.93
SVM decision value 1.85
SVM RNA-class probability 0.980068
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10514160 119 - 20766785
CUUUGGCAUCUGAUAAUUUCUACGAUUUUCAUGGCUGGCCGUGGCAAUUUGAUUUUAGUUUUCACCAUGAUGCCACGUUUUGGCCGUCUAUCGAUGCGGCUUUUUUGGUCGGUAUUGAA-
....(((...(((.((((.....)))).))).(((..(.(((((((...((..............))...)))))))..)..))))))..(((((((((((.....)))).))))))).- ( -32.24)
>DroSec_CAF1 14746 120 - 1
CUUUGGCAUCUGAUAAUUUCCACGAUUUUCAUGGCUGGCCGUAGCAAUUUGAUUUUAGUUUUCACCAUGAUGCCACGUUUUGGCCGUCUAUCGAUGCGGCUUUUUUGGCCGGUAUUGAAA
...((((((((((.((((....(((.((.(((((....)))).).)).))).....)))).)))....)))))))...............(((((((((((.....)))).))))))).. ( -28.90)
>DroSim_CAF1 9767 120 - 1
CUUUGGCAUCUGAUAAUUUCCACGAUUUUCAUGGCUGGCCGUGGCAAUUUGAUUUUAGUUUUCACCAUGAUGCCACGUUUUGGCCGUCUAUCGAUGCGGCUUUUUUGGCCGGUAUUGAAA
....(((...(((.((((.....)))).))).(((..(.(((((((...((..............))...)))))))..)..))))))..(((((((((((.....)))).))))))).. ( -34.94)
>DroEre_CAF1 14892 119 - 1
CUUUGGCAUCUGAUAAUUUUCACGAUUUUCAUGGCUGGCCGUGGCAAUUUGAUUUUAGUUUUCACCAUGAUGCCACGUUUUGGCCGUCUAUCGAUGCGGCUUUUUUGGCGGGCAUUGAA-
...(((....(((.((((.(((.((((.((((((....)))))).)))))))....)))).)))))).((((((.((((..((((((........)))))).....))))))))))...- ( -34.50)
>DroYak_CAF1 11458 118 - 1
CUUUGGCAUCUGAUAAUUUCCACGAUUUUCAUCGCUGGCCGUGGCAAUUUGAUUUUAGUUUUCACCAUGAUGCCACGUUCGGGCCGUCUAUCGAUGCGGCUUU-UUGGCCGAUAUUGAA-
....(((...............((((....))))(((..(((((((...((..............))...)))))))..)))))).....(((((((((((..-..))))).)))))).- ( -35.74)
>consensus
CUUUGGCAUCUGAUAAUUUCCACGAUUUUCAUGGCUGGCCGUGGCAAUUUGAUUUUAGUUUUCACCAUGAUGCCACGUUUUGGCCGUCUAUCGAUGCGGCUUUUUUGGCCGGUAUUGAA_
....(((...(((.((((.....)))).))).(((..(.(((((((...((..............))...)))))))..)..))))))..(((((((((((.....))))).)))))).. (-30.96 = -31.08 +   0.12)

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 10:46:07 2006