Locus 6153

Sequence ID 3R_DroMel_CAF1
Location 16,117,092 – 16,117,345
Length 253
Max. P 0.993502
window10028 window10029 window10030 window10031 window10032

overview

Window 8

Location 16,117,092 – 16,117,198
Length 106
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 76.12
Mean single sequence MFE -27.98
Consensus MFE -13.43
Energy contribution -15.76
Covariance contribution 2.33
Combinations/Pair 1.10
Mean z-score -1.85
Structure conservation index 0.48
SVM decision value 0.09
SVM RNA-class probability 0.577235
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16117092 106 + 27905053
UAGGGUCCGAAGAACU-UUUGUGCACCCUACUUAGCUGGGGGACCGCUCUUCCUCAAUCCCCUCAUUCAGAGCUCCCCCAUUAAGGUAUUUCUUCGGAAUGCAGAAG
((((((((((((...)-)))).).))))))(((((.(((((((..(((((..................)))))))))))))))))(((((.(....))))))..... ( -34.97)
>DroPse_CAF1 78221 87 + 1
UCGAAACUGGUCAACUCUAUAUGCACCCUACAUAUC----------AUAUUCCCACUCCCU----A------AUCCACUACUAAAAUACGUUUAGGGAAUGUAGAAG
........(((((........)).)))((((((...----------..........(((((----(------(..................)))))))))))))... ( -12.98)
>DroSec_CAF1 67774 102 + 1
UAGGGACCGAAGAACU-UUUGUGCACCCUACUUAGCUGGGGGAACGCUCUUCCCCUUUCAC----AACAGAGCUCCCCCAUUAAGGUAUUUCUUCGGAAUGCAGAAG
(((((.((((((...)-)))).)..)))))(((((.(((((((..(((((...........----...)))))))))))))))))(((((.(....))))))..... ( -32.34)
>DroSim_CAF1 74053 102 + 1
UAGGGACCGAAGAACU-UUUGUGCACCCUACUUAGCUGGGGGAACGCUCUUCCCCUUUCAA----AACAGAGCUCCCCCAUUAAGGUAUUUCUUCGGAAUGCAGAAG
(((((.((((((...)-)))).)..)))))(((((.(((((((..(((((...........----...)))))))))))))))))(((((.(....))))))..... ( -32.34)
>DroEre_CAF1 44607 106 + 1
UAGGGCCUGAAGAACU-UUUGUGCACCCUACUUAGCGGGGGGAACGUUCUUCCCCAAUACCCUUUUACAGUUUUCCCCCAUUAAGGUAUCUCUUCGGAAUGCAGAAG
(((((..((....((.-...)).)))))))(((((.(((((((((........................).)))))))).)))))((((.((....))))))..... ( -26.26)
>DroYak_CAF1 88068 106 + 1
UAGGAACCAAAGAACU-UUUGUGCACCCUACCUAGCUGGGGGAACGAUCUUCCCCAAUCCCCUUUUACAGAGUUCCCCCAUUAAGGUAUCUCUUCGGAAUGCAGAAG
..............((-(((((......(((((.(.(((((((((..........................))))))))).).)))))..((....))..))))))) ( -28.97)
>consensus
UAGGGACCGAAGAACU_UUUGUGCACCCUACUUAGCUGGGGGAACGCUCUUCCCCAAUCCC____AACAGAGCUCCCCCAUUAAGGUAUUUCUUCGGAAUGCAGAAG
......(((((((((.....))......(((((...(((((((..............................)))))))...)))))..))))))).......... (-13.43 = -15.76 +   2.33)

alignment

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secondary structure

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Window 9

Location 16,117,092 – 16,117,198
Length 106
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 76.12
Mean single sequence MFE -32.50
Consensus MFE -17.91
Energy contribution -20.29
Covariance contribution 2.38
Combinations/Pair 1.21
Mean z-score -1.86
Structure conservation index 0.55
SVM decision value 0.71
SVM RNA-class probability 0.829717
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16117092 106 - 27905053
CUUCUGCAUUCCGAAGAAAUACCUUAAUGGGGGAGCUCUGAAUGAGGGGAUUGAGGAAGAGCGGUCCCCCAGCUAAGUAGGGUGCACAAA-AGUUCUUCGGACCCUA
.........(((((((((.(((((((.((((((((((((...(.((....)).)...)))))..)))))))......)))))))......-..)))))))))..... ( -37.40)
>DroPse_CAF1 78221 87 - 1
CUUCUACAUUCCCUAAACGUAUUUUAGUAGUGGAU------U----AGGGAGUGGGAAUAU----------GAUAUGUAGGGUGCAUAUAGAGUUGACCAGUUUCGA
.((((.((((((((((.(.((((.....))))).)------)----))))))))))))..(----------((.((....(((.((........))))).)).))). ( -20.30)
>DroSec_CAF1 67774 102 - 1
CUUCUGCAUUCCGAAGAAAUACCUUAAUGGGGGAGCUCUGUU----GUGAAAGGGGAAGAGCGUUCCCCCAGCUAAGUAGGGUGCACAAA-AGUUCUUCGGUCCCUA
..........((((((((.(((((((.((((((((((((.((----.(....).)).)))))..)))))))......)))))))......-..))))))))...... ( -36.80)
>DroSim_CAF1 74053 102 - 1
CUUCUGCAUUCCGAAGAAAUACCUUAAUGGGGGAGCUCUGUU----UUGAAAGGGGAAGAGCGUUCCCCCAGCUAAGUAGGGUGCACAAA-AGUUCUUCGGUCCCUA
..........((((((((.(((((((.((((((((((((.((----((....)))).)))))..)))))))......)))))))......-..))))))))...... ( -37.40)
>DroEre_CAF1 44607 106 - 1
CUUCUGCAUUCCGAAGAGAUACCUUAAUGGGGGAAAACUGUAAAAGGGUAUUGGGGAAGAACGUUCCCCCCGCUAAGUAGGGUGCACAAA-AGUUCUUCAGGCCCUA
((((........)))).((((((((..((.((.....)).))..))))))))((((((((((((.(((..(.....)..))).)).....-.)))))))...))).. ( -27.90)
>DroYak_CAF1 88068 106 - 1
CUUCUGCAUUCCGAAGAGAUACCUUAAUGGGGGAACUCUGUAAAAGGGGAUUGGGGAAGAUCGUUCCCCCAGCUAGGUAGGGUGCACAAA-AGUUCUUUGGUUCCUA
((((........))))...(((((...((((((((((((.....))).((((......)))))))))))))...)))))(((.((.((((-.....)))))).))). ( -35.20)
>consensus
CUUCUGCAUUCCGAAGAAAUACCUUAAUGGGGGAGCUCUGUA____GGGAAUGGGGAAGAGCGUUCCCCCAGCUAAGUAGGGUGCACAAA_AGUUCUUCGGUCCCUA
..........((((((((.(((((((.(((((((((..........................)))))))))......))))))).........))))))))...... (-17.91 = -20.29 +   2.38)

alignment

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secondary structure

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Window 0

Location 16,117,124 – 16,117,226
Length 102
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 77.86
Mean single sequence MFE -26.62
Consensus MFE -19.62
Energy contribution -20.68
Covariance contribution 1.06
Combinations/Pair 1.15
Mean z-score -1.36
Structure conservation index 0.74
SVM decision value 0.73
SVM RNA-class probability 0.834153
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16117124 102 + 27905053
AGCUGGGGGACCGCUCUUCCUCAAUCCCCUCAUUC---AGAGCUCCCCCAUUAAGGUAUUUCUUCGGAAUGCAGAAGACGCGACGGUCUUUCAUUCA-----GAACCGGA
...(((((((..(((((..................---))))))))))))....(((...(((...(((((..((((((......))))))))))))-----)))))... ( -29.87)
>DroSec_CAF1 67806 98 + 1
AGCUGGGGGAACGCUCUUCCCCUUUCAC----AAC---AGAGCUCCCCCAUUAAGGUAUUUCUUCGGAAUGCAGAAGACACGAAGGUCUUUCAUUCA-----GAACCGGA
...(((((((..(((((...........----...---))))))))))))....(((...(((...(((((..((((((......))))))))))))-----)))))... ( -29.94)
>DroSim_CAF1 74085 98 + 1
AGCUGGGGGAACGCUCUUCCCCUUUCAA----AAC---AGAGCUCCCCCAUUAAGGUAUUUCUUCGGAAUGCAGAAGACACGAAGGUCUUUCAUUCA-----GAACCGGA
...(((((((..(((((...........----...---))))))))))))....(((...(((...(((((..((((((......))))))))))))-----)))))... ( -29.94)
>DroEre_CAF1 44639 101 + 1
AGCGGGGGGAACGUUCUUCCCCAAUACCCUUUUAC---AGUUUUCCCCCAUUAAGGUAUCUCUUCGGAAUGCAGAAGACAGG-AGGUCUUUCAUUCA-----GAACCGGA
..(((((((((.....)))))).(((((.......---................)))))...(((.(((((..((((((...-..))))))))))).-----)))))).. ( -25.80)
>DroYak_CAF1 88100 102 + 1
AGCUGGGGGAACGAUCUUCCCCAAUCCCCUUUUAC---AGAGUUCCCCCAUUAAGGUAUCUCUUCGGAAUGCAGAAGACAGGAAGGUCUUUCAUUCA-----GAACCGGA
...(((((((((.......................---...)))))))))....(((.(((.....(((((..((((((......))))))))))))-----)))))... ( -28.27)
>DroAna_CAF1 44111 102 + 1
UUCC----AAUCGCUCUUCUACCUUUAA----GCCAUAAAUGGUUCUCCAUAAAAAUAUUCCUUAGGAAUGCCGAAGAAAUAAACUUCUUUCAUUCAAGCCUGAACCGGA
.(((----....(((............)----)).......(((((..........((((((...))))))..((((((......))))))...........)))))))) ( -15.90)
>consensus
AGCUGGGGGAACGCUCUUCCCCAAUCAC____UAC___AGAGCUCCCCCAUUAAGGUAUUUCUUCGGAAUGCAGAAGACACGAAGGUCUUUCAUUCA_____GAACCGGA
....((((((..(((((.....................))))))))))).....(((.((......(((((..((((((......)))))))))))......)))))... (-19.62 = -20.68 +   1.06)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,117,124 – 16,117,226
Length 102
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 77.86
Mean single sequence MFE -30.30
Consensus MFE -19.31
Energy contribution -19.60
Covariance contribution 0.28
Combinations/Pair 1.27
Mean z-score -1.23
Structure conservation index 0.64
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16117124 102 - 27905053
UCCGGUUC-----UGAAUGAAAGACCGUCGCGUCUUCUGCAUUCCGAAGAAAUACCUUAAUGGGGGAGCUCU---GAAUGAGGGGAUUGAGGAAGAGCGGUCCCCCAGCU
..((((.(-----(.......))))))..((.(((((........)))))..........((((((((((((---...(.((....)).)...)))))..))))))))). ( -31.40)
>DroSec_CAF1 67806 98 - 1
UCCGGUUC-----UGAAUGAAAGACCUUCGUGUCUUCUGCAUUCCGAAGAAAUACCUUAAUGGGGGAGCUCU---GUU----GUGAAAGGGGAAGAGCGUUCCCCCAGCU
...(((((-----((((((.(((((......)))))...)))))...)))...)))....((((((((((((---.((----.(....).)).)))))..)))))))... ( -32.20)
>DroSim_CAF1 74085 98 - 1
UCCGGUUC-----UGAAUGAAAGACCUUCGUGUCUUCUGCAUUCCGAAGAAAUACCUUAAUGGGGGAGCUCU---GUU----UUGAAAGGGGAAGAGCGUUCCCCCAGCU
...(((((-----((((((.(((((......)))))...)))))...)))...)))....((((((((((((---.((----((....)))).)))))..)))))))... ( -32.80)
>DroEre_CAF1 44639 101 - 1
UCCGGUUC-----UGAAUGAAAGACCU-CCUGUCUUCUGCAUUCCGAAGAGAUACCUUAAUGGGGGAAAACU---GUAAAAGGGUAUUGGGGAAGAACGUUCCCCCCGCU
..((((((-----.(((((.(((((..-...)))))...))))).)))..((((((((..((.((.....))---.))..))))))))((((((.....))))))))).. ( -31.20)
>DroYak_CAF1 88100 102 - 1
UCCGGUUC-----UGAAUGAAAGACCUUCCUGUCUUCUGCAUUCCGAAGAGAUACCUUAAUGGGGGAACUCU---GUAAAAGGGGAUUGGGGAAGAUCGUUCCCCCAGCU
...(((((-----((((((.(((((......)))))...))))).....))).)))....((((((((((((---.....))).((((......)))))))))))))... ( -31.30)
>DroAna_CAF1 44111 102 - 1
UCCGGUUCAGGCUUGAAUGAAAGAAGUUUAUUUCUUCGGCAUUCCUAAGGAAUAUUUUUAUGGAGAACCAUUUAUGGC----UUAAAGGUAGAAGAGCGAUU----GGAA
((((((((..(((.(((.((((........))))))))))..(((((((((...)))))).))))))))....((.((----((..........)))).)).----))). ( -22.90)
>consensus
UCCGGUUC_____UGAAUGAAAGACCUUCGUGUCUUCUGCAUUCCGAAGAAAUACCUUAAUGGGGGAGCUCU___GUA____GGGAAUGGGGAAGAGCGUUCCCCCAGCU
...(((........(((((.(((((......)))))...))))).........)))....(((((((((.............................)))))))))... (-19.31 = -19.60 +   0.28)

alignment

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secondary structure

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Window 2

Location 16,117,226 – 16,117,345
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 92.86
Mean single sequence MFE -31.20
Consensus MFE -26.62
Energy contribution -26.38
Covariance contribution -0.24
Combinations/Pair 1.19
Mean z-score -2.16
Structure conservation index 0.85
SVM decision value 2.40
SVM RNA-class probability 0.993502
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16117226 119 - 27905053
GGUCAAAUAAGCCUCUUUAUGGGUACGAAUUUACUGUUCAGAAGGAGCUUGACAAGACCUUUACCUUAGGCCUGCAUUUUAUGGUCUUAUAAACGAGACUUUUUUCAGUGCUUAAGAAA
((((...(((((.(((((.((..((.(......)))..)).))))))))))....)))).....((((((((((........((((((......)))))).....))).)))))))... ( -32.12)
>DroSec_CAF1 67904 119 - 1
GGUCAAAUAAGCCUCUUUAUGGGUACGAAUUUACUCUACAGGAGGAGCUUGACAAGCCCUUUACCUUAGGCCUGCAUUUUAUGGUCUUAUAAACGAGACUUUUUUCAGUGCCUAAGAAA
.(((((.....((((((...(((((......)))))...))))))...)))))...........((((((((((........((((((......)))))).....))).)))))))... ( -35.72)
>DroSim_CAF1 74183 119 - 1
GGUCAAAUAAGCCUCUUUAUGGGUACGAAUAUACUCUACAGGAGGAGCUUGACAAGCCCUUUACCUUAGGCCUGCAUUCUAUGGUCUUAUAAACGAGACUUUUUUCAGUGCCUAAGAAA
.(((((.....((((((...(((((......)))))...))))))...)))))...........((((((((((........((((((......)))))).....))).)))))))... ( -35.62)
>DroEre_CAF1 44740 119 - 1
GGUCAAAAAAGCCUCUUUAUUGCUACGUAUUUACUGUUCAGAAGGAGCUUGACAAGCCCUUUACUUUAGGCCUGCAUUUUAUGGUCUUAUAAACGAGACUUUUUUCAGUGCCUGAGAAA
(((.....((((..((((...((............))...))))..)))).....)))......((((((((((........((((((......)))))).....))).)))))))... ( -27.62)
>DroYak_CAF1 88202 118 - 1
GGUCAAAUAAGCCUCUUUAUUGAUACGAAUUUACUGUUCAAAAGAAGCUCGACAAGC-CUUUACUUAAGGCCUGCAUUUUAUGGUCUUAUAAACGAGACUUUUUUCAGUGCCUAAGAAA
(((......(((.(((((..(((.(((.......))))))))))).)))......))-)....((((.((((((........((((((......)))))).....))).)))))))... ( -24.92)
>consensus
GGUCAAAUAAGCCUCUUUAUGGGUACGAAUUUACUGUUCAGAAGGAGCUUGACAAGCCCUUUACCUUAGGCCUGCAUUUUAUGGUCUUAUAAACGAGACUUUUUUCAGUGCCUAAGAAA
.((((....(((..((((..(((((......)))))....))))..)))))))...........((((((((((........((((((......)))))).....))).)))))))... (-26.62 = -26.38 +  -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 12:14:03 2006