Locus 5786

Sequence ID 2L_DroMel_CAF1
Location 16,399,674 – 16,399,925
Length 251
Max. P 0.875381
window9173 window9174 window9175

overview

Window 3

Location 16,399,674 – 16,399,794
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 83.26
Mean single sequence MFE -29.14
Consensus MFE -19.63
Energy contribution -21.87
Covariance contribution 2.24
Combinations/Pair 1.04
Mean z-score -2.29
Structure conservation index 0.67
SVM decision value 0.28
SVM RNA-class probability 0.667045
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16399674 120 + 22407834
UUCUCCACUUACACAAAAAUUUACAUUUGAUUGCUGUUCAAUCAACUCUCAUCGCUGGCGACCCACAGAGUUCAACAUGUGAUAUCCUUGACAUUUAUGAGUUGUUGGCUCUGUGGGACC
..........................(((((((.....)))))))......(((....)))((((((((((.(((((..(.(((...........))).)..)))))))))))))))... ( -30.50)
>DroSec_CAF1 24129 118 + 1
UUCUCCACUUACA--GAAAUUUACAUUUGAUUGCUGUUCAAUCAACUCUCAUCGCUGGCGACCCACAGAGUUCAACAUGUGAUAUCCUUGACAUUUAUGAGCUGUUGGCUCUGUGGGACC
...........((--(..........(((((((.....))))))).........)))....((((((((((.(((((.((.(((...........)))..)))))))))))))))))... ( -31.21)
>DroSim_CAF1 22874 118 + 1
UUCUCCACUUACA--GAAAUUUACAUUUGAUUGCUGUUCAAUCAACUCUCAUCGCUGGCGACCCACAGAGUUCAACAUGUGAUAUCCUUGACAUUUAUGAGUUGUUGGCUCUGUGGGACC
...........((--(..........(((((((.....))))))).........)))....((((((((((.(((((..(.(((...........))).)..)))))))))))))))... ( -31.11)
>DroEre_CAF1 20263 92 + 1
UUCUCCACUUAUG--GCAAUUUACAUUUGAUUGCUGUUCAAUCAACUC--------------CCACAGAGCUCAACAUGUGAUAUCCCUGACAUUUAUGAGUUCCUGA------------
..........(((--((((((.......)))))))))...........--------------...(((((((((..((((.(......).))))...)))))).))).------------ ( -17.80)
>DroYak_CAF1 24875 118 + 1
UUCUCUAUUCACA--GAAAUUUACAUUUGAUUGCUGUUCAAUCAACUCUCAUCGCUGGCGACCCACAGAGUUCAACAUGUGAUAUCCUUGACAUUUAUGAGAUGUUGGCUCUGUGGGACC
........((.((--(..........(((((((.....))))))).........)))..))((((((((((.((((((.(.(((...........))).).))))))))))))))))... ( -34.81)
>DroAna_CAF1 19021 118 + 1
GGCUCCUUUUCGA--GCAAUUUACAUUCGAUUACUGUCCUAUCUACUUUGAUCACUGACAACCCACAGAGUUCAACAUGUGAUAUCCUUGACAGUUAUGAGUUGUUGGCCCUGUGGGUCC
.((((......))--)).................((((..(((......)))....))))((((((((.(..(((((..(.(((...........))).)..)))))..))))))))).. ( -29.40)
>consensus
UUCUCCACUUACA__GAAAUUUACAUUUGAUUGCUGUUCAAUCAACUCUCAUCGCUGGCGACCCACAGAGUUCAACAUGUGAUAUCCUUGACAUUUAUGAGUUGUUGGCUCUGUGGGACC
..........................(((((((.....)))))))................(((((((((.((((((..(.(((...........))).)..)))))))))))))))... (-19.63 = -21.87 +   2.24)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,399,714 – 16,399,827
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.81
Mean single sequence MFE -29.86
Consensus MFE -24.36
Energy contribution -25.24
Covariance contribution 0.88
Combinations/Pair 1.04
Mean z-score -1.75
Structure conservation index 0.82
SVM decision value 0.89
SVM RNA-class probability 0.875381
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16399714 113 + 22407834
AUCAACUCUCAUCGCUGGCGACCCACAGAGUUCAACAUGUGAUAUCCUUGACAUUUAUGAGUUGUUGGCUCUGUGGGACCCCCGUUCCCCUA-------UACAAAAUAACAUGUUAGAUC
..............((((((.((((((((((.(((((..(.(((...........))).)..)))))))))))))))......((.......-------.)).........))))))... ( -28.20)
>DroSec_CAF1 24167 113 + 1
AUCAACUCUCAUCGCUGGCGACCCACAGAGUUCAACAUGUGAUAUCCUUGACAUUUAUGAGCUGUUGGCUCUGUGGGACCCCCGCUCCCCUA-------UACAAAGUAACAUGUUAGAUC
.............((.((.(.((((((((((.(((((.((.(((...........)))..))))))))))))))))).).)).))....(((-------.(((........))))))... ( -29.90)
>DroSim_CAF1 22912 113 + 1
AUCAACUCUCAUCGCUGGCGACCCACAGAGUUCAACAUGUGAUAUCCUUGACAUUUAUGAGUUGUUGGCUCUGUGGGACCCCCGCUCCCCUA-------UACAAAGUAACAUGUUAGAUC
.............((.((.(.((((((((((.(((((..(.(((...........))).)..))))))))))))))).).)).))....(((-------.(((........))))))... ( -29.80)
>DroYak_CAF1 24913 113 + 1
AUCAACUCUCAUCGCUGGCGACCCACAGAGUUCAACAUGUGAUAUCCUUGACAUUUAUGAGAUGUUGGCUCUGUGGGACCCCCGCUCCCCUA-------UACAACGUAACAUGUUAGAUC
.............((.((.(.((((((((((.((((((.(.(((...........))).).)))))))))))))))).).)).))....(((-------.(((........))))))... ( -33.30)
>DroAna_CAF1 19059 120 + 1
AUCUACUUUGAUCACUGACAACCCACAGAGUUCAACAUGUGAUAUCCUUGACAGUUAUGAGUUGUUGGCCCUGUGGGUCCCCCACUCUACUAUGUCCUCUGUAAGGAAGCAUGUUAUAUC
.........((.(.(((........))).).))(((((((....(((((((((.....((((.(..(((((...)))))..).)))).....))))......))))).)))))))..... ( -28.10)
>consensus
AUCAACUCUCAUCGCUGGCGACCCACAGAGUUCAACAUGUGAUAUCCUUGACAUUUAUGAGUUGUUGGCUCUGUGGGACCCCCGCUCCCCUA_______UACAAAGUAACAUGUUAGAUC
.............((.((.(.((((((((((.(((((..(.(((...........))).)..))))))))))))))).).)).))................................... (-24.36 = -25.24 +   0.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 16,399,827 – 16,399,925
Length 98
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 81.09
Mean single sequence MFE -19.74
Consensus MFE -16.30
Energy contribution -15.74
Covariance contribution -0.56
Combinations/Pair 1.24
Mean z-score -1.57
Structure conservation index 0.83
SVM decision value 0.37
SVM RNA-class probability 0.708370
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16399827 98 - 22407834
--AAAAGAAAUCCAGU--AACUGACAGAAGCAACAGGGAUA--------------UAAGAAACUCACGAGGAAUGUUUCAGUGUUAUGCAAAUAAUAUCUGUCAUUUCUCGUUGUU
--.......((((.((--..((......))..))..)))).--------------.....(((..((((((((((...(((((((((....)))))).))).)))))))))).))) ( -23.30)
>DroSec_CAF1 24280 97 - 1
--AAA-AAAAUCCAGU--AACUGACAGAAGCAACAGGGAUA--------------UAAGAAACUCACGAGGAAUGUUCCAGUGUUAUGCAAAUAAUAUCUGUCAUUUCUCGUUGUU
--...-...((((.((--..((......))..))..)))).--------------.....(((..((((((((((...(((((((((....)))))).))).)))))))))).))) ( -22.60)
>DroSim_CAF1 23025 95 - 1
----A-AAAAUCCAGU--AACUGACAGAAGCAACAGGGAUA--------------UAAGAAACUCACGAGGAAUGUUUCAGUGUUAUGCAAAUAAUAUCUGUCAUUUCUCGUUGUU
----.-...((((.((--..((......))..))..)))).--------------.....(((..((((((((((...(((((((((....)))))).))).)))))))))).))) ( -23.30)
>DroYak_CAF1 25026 94 - 1
------AAAAUCCAGU--AACCGACAGAAGCAACAGGAAUA--------------CAAAAAACUCAUGAAGAAUGUUUCAGUGUUAUGCAAAUAAUAUCUGUCAUUUUGUGUUGUU
------..........--..........((((((((.....--------------).............((((((...(((((((((....)))))).))).)))))).))))))) ( -14.10)
>DroAna_CAF1 19179 116 - 1
GAAAAAAACACACAGUCUCACUGACAGAAGCAACAGGGAAGUUACUGAACAACAAAAAAAAACUCAUAAGGAAUGUUUCAAUGUUAUGCAAAUCAUAUUUGACAUUUGUUAUUGUU
..............(((.....)))...((((((((........)))...................(((.(((((((..(((((.((....)).))))).))))))).)))))))) ( -15.40)
>consensus
__AAA_AAAAUCCAGU__AACUGACAGAAGCAACAGGGAUA______________UAAGAAACUCACGAGGAAUGUUUCAGUGUUAUGCAAAUAAUAUCUGUCAUUUCUCGUUGUU
............(((.....))).....................................(((..((((((((((...(((((((((....)))))).))).)))))))))).))) (-16.30 = -15.74 +  -0.56)

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 11:52:51 2006