Locus 688

Sequence ID 3R_DroMel_CAF1
Location 2,463,297 – 2,463,690
Length 393
Max. P 0.984964
window1090 window1091 window1092 window1093 window1094

overview

Window 0

Location 2,463,297 – 2,463,416
Length 119
Sequences 4
Columns 119
Reading direction reverse
Mean pairwise identity 98.46
Mean single sequence MFE -35.50
Consensus MFE -35.01
Energy contribution -34.83
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -1.90
Structure conservation index 0.99
SVM decision value 0.55
SVM RNA-class probability 0.779576
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2463297 119 - 27905053
ACAGAAUGUUGCCCUGCCAACGCGGCACGUGGAACGUGGCCAGAUUAUGCUGCAUUAUCACCUGUAAAUCCUUAUUGGCAAUCAAAACUUUGCCAACAGCGCUGGUCCUGACCAUCUCC
.(((.(((((.(((((((.....)))).).)))))))((((((....(((((..((((.....)))).......(((((((........)))))))))))))))))))))......... ( -34.00)
>DroSec_CAF1 22271 119 - 1
ACAGAAUGUUGCCCUGCCAACGCGGCACGUGGAACGUGGCCAGAUUAUGCUGUAUUAUCACCUGUAAAUCCUUAUUGGCAAUCAAAACUUUGCCAACAGCGCUGGUCCUGACCAGCUCC
.(((.(((((.(((((((.....)))).).)))))))((((((....((((((.((((.....))))........((((((........)))))))))))))))))))))......... ( -35.10)
>DroSim_CAF1 19011 119 - 1
ACAGAAUGUUGCCCUGCCAACGCGGCACGUGGAACGUGGCCAGAUUAUGCUGUAUUAUCACCUGUAAAUCCUUAUUGGCAAUCAAAACUUUGCCAACAGCGCUGGUCCUGACCAGCUCC
.(((.(((((.(((((((.....)))).).)))))))((((((....((((((.((((.....))))........((((((........)))))))))))))))))))))......... ( -35.10)
>DroEre_CAF1 23715 119 - 1
ACAGAAUGUUGCCCUGCCAACGCGGCACGUGGAACGUGGCCAGAUUAUGCUGUAUUAUCACCUGUAAAUCCUUAUUGGCAAUCAAAACUUUGCCAACAGCGCUGGCCCUGACCAACUCC
.(((.(((((.(((((((.....)))).).)))))))((((((....((((((.((((.....))))........((((((........)))))))))))))))))))))......... ( -37.80)
>consensus
ACAGAAUGUUGCCCUGCCAACGCGGCACGUGGAACGUGGCCAGAUUAUGCUGUAUUAUCACCUGUAAAUCCUUAUUGGCAAUCAAAACUUUGCCAACAGCGCUGGUCCUGACCAGCUCC
.(((.(((((.(((((((.....)))).).)))))))((((((....(((((..((((.....)))).......(((((((........)))))))))))))))))))))......... (-35.01 = -34.83 +  -0.19)

alignment

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secondary structure

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Window 1

Location 2,463,416 – 2,463,536
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 97.36
Mean single sequence MFE -27.92
Consensus MFE -27.20
Energy contribution -27.20
Covariance contribution -0.00
Combinations/Pair 1.04
Mean z-score -1.51
Structure conservation index 0.97
SVM decision value 0.03
SVM RNA-class probability 0.550598
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2463416 120 - 27905053
UUUCGAAAUCCAUUUUAAUGCAUUUCGCUCCACUCUUUUCCGCGCAUGCAGCUCGCAAAAGAAAAGCGGGUAAAAGCCGGGAGCACAAGGUAACUACAAAAUUCCAGAUACAAUUUUACA
....(((((.(((....))).)))))(((((..((((((.((.((.....)).)).))))))....(((.......)))))))).................................... ( -25.30)
>DroSec_CAF1 22390 120 - 1
UUUCGAAAUCCAUUUUAAUGCAUUUCGCUCCACUCUUUUCCGCGCAUGCAGCUCGCAAAGGAAAAGCGGGUAAAAGCCGGGAGCACAAGGUAACUACAAAAUUCCAGAUACAAUUUUACA
....(((((.(((....))).)))))(((((.(.(((((((.....(((.....)))..))))))).)(((....))).))))).................................... ( -27.20)
>DroSim_CAF1 19130 120 - 1
UUUCGAAAUCCAUUUUAAUGCAUUUCGCUCCACACUUUUCCGCGGAUGCAGCUCGCAAAGGAAAAGCGGGCAAAAGCCGGGAGCACAAGGUAACUACAAAAUUCCAGAUACAAUUUUACA
....(((((.(((....))).)))))(((((.(.(((((((((((.......))))...))))))).)(((....))).))))).................................... ( -30.10)
>DroEre_CAF1 23834 120 - 1
UUUCGAAAUCCAUUUUAAUGCAUUUCGCUCCACUCUUUUCCGCGCAUGCAGCUCGCAAAGGAAAAGCGGGCAAAAGCCGGGAGCACAAGGUAACUACAAUUUUCCAGAUACAAUUUUACA
....(((((.(((....))).)))))(((((.(.(((((((.....(((.....)))..))))))).)(((....))).))))).................................... ( -29.10)
>consensus
UUUCGAAAUCCAUUUUAAUGCAUUUCGCUCCACUCUUUUCCGCGCAUGCAGCUCGCAAAGGAAAAGCGGGCAAAAGCCGGGAGCACAAGGUAACUACAAAAUUCCAGAUACAAUUUUACA
....(((((.(((....))).)))))(((((.(.(((((((.....(((.....)))..))))))).)(((....))).))))).................................... (-27.20 = -27.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,463,496 – 2,463,610
Length 114
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 96.86
Mean single sequence MFE -26.64
Consensus MFE -26.46
Energy contribution -26.27
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.22
Structure conservation index 0.99
SVM decision value 1.52
SVM RNA-class probability 0.960588
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2463496 114 + 27905053
GAAAAGAGUGGAGCGAAAUGCAUUAAAAUGGAUUUCGAAACUUUAAAACUCAAUUUCAAUUGCACAGAAAAAGUUUCGCUCUGCGAUUUGCAUAUUUACGUGAAAGGGAGCGGG
(.(((..(..(((((((((.(((....))).)))))((((((((......((((....)))).......))))))))))))..)..))).).......(((........))).. ( -27.52)
>DroSec_CAF1 22470 109 + 1
GAAAAGAGUGGAGCGAAAUGCAUUAAAAUGGAUUUCGAAACUUUAAAACUCAAUUUCAAUUGCACAGAAAAAGUUUCGCUCUGCGAUUUGCAUAUUUACGUGAAAGGGA-----
.......(..(((((((((.(((....))).)))))((((((((......((((....)))).......))))))))))))..)..((..(........)..)).....----- ( -26.22)
>DroSim_CAF1 19210 109 + 1
GAAAAGUGUGGAGCGAAAUGCAUUAAAAUGGAUUUCGAAACUUUAAAACUCAAUUUCAAUUGCACAGAAAAAGUUUCGCUCUGCGAUUUGCAUAUUUACGUGGAAGGGA-----
......((..(((((((((.(((....))).)))))((((((((......((((....)))).......))))))))))))..)).((..(........)..)).....----- ( -26.62)
>DroEre_CAF1 23914 109 + 1
GAAAAGAGUGGAGCGAAAUGCAUUAAAAUGGAUUUCGAAACUUUAAAACUCAAUUUCAAUUGCACAGAAAAAGUUUCGCUCUGCGAUUUGCAUAUUUACGUGAAAGGGA-----
.......(..(((((((((.(((....))).)))))((((((((......((((....)))).......))))))))))))..)..((..(........)..)).....----- ( -26.22)
>consensus
GAAAAGAGUGGAGCGAAAUGCAUUAAAAUGGAUUUCGAAACUUUAAAACUCAAUUUCAAUUGCACAGAAAAAGUUUCGCUCUGCGAUUUGCAUAUUUACGUGAAAGGGA_____
.......(..(((((((((.(((....))).)))))((((((((......((((....)))).......))))))))))))..)..((..(........)..)).......... (-26.46 = -26.27 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,463,496 – 2,463,610
Length 114
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 96.86
Mean single sequence MFE -21.34
Consensus MFE -21.32
Energy contribution -21.32
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 1.00
SVM decision value 1.13
SVM RNA-class probability 0.920091
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2463496 114 - 27905053
CCCGCUCCCUUUCACGUAAAUAUGCAAAUCGCAGAGCGAAACUUUUUCUGUGCAAUUGAAAUUGAGUUUUAAAGUUUCGAAAUCCAUUUUAAUGCAUUUCGCUCCACUCUUUUC
......................(((.....)))((((((((((((.......((((....))))......))))))))(((((.(((....))).))))))))).......... ( -21.32)
>DroSec_CAF1 22470 109 - 1
-----UCCCUUUCACGUAAAUAUGCAAAUCGCAGAGCGAAACUUUUUCUGUGCAAUUGAAAUUGAGUUUUAAAGUUUCGAAAUCCAUUUUAAUGCAUUUCGCUCCACUCUUUUC
-----.................(((.....)))((((((((((((.......((((....))))......))))))))(((((.(((....))).))))))))).......... ( -21.32)
>DroSim_CAF1 19210 109 - 1
-----UCCCUUCCACGUAAAUAUGCAAAUCGCAGAGCGAAACUUUUUCUGUGCAAUUGAAAUUGAGUUUUAAAGUUUCGAAAUCCAUUUUAAUGCAUUUCGCUCCACACUUUUC
-----..........((.....(((.....)))((((((((((((.......((((....))))......))))))))(((((.(((....))).))))))))).))....... ( -21.42)
>DroEre_CAF1 23914 109 - 1
-----UCCCUUUCACGUAAAUAUGCAAAUCGCAGAGCGAAACUUUUUCUGUGCAAUUGAAAUUGAGUUUUAAAGUUUCGAAAUCCAUUUUAAUGCAUUUCGCUCCACUCUUUUC
-----.................(((.....)))((((((((((((.......((((....))))......))))))))(((((.(((....))).))))))))).......... ( -21.32)
>consensus
_____UCCCUUUCACGUAAAUAUGCAAAUCGCAGAGCGAAACUUUUUCUGUGCAAUUGAAAUUGAGUUUUAAAGUUUCGAAAUCCAUUUUAAUGCAUUUCGCUCCACUCUUUUC
......................(((.....)))((((((((((((.......((((....))))......))))))))(((((.(((....))).))))))))).......... (-21.32 = -21.32 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,463,570 – 2,463,690
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.87
Mean single sequence MFE -34.12
Consensus MFE -31.26
Energy contribution -31.14
Covariance contribution -0.12
Combinations/Pair 1.06
Mean z-score -2.53
Structure conservation index 0.92
SVM decision value 1.99
SVM RNA-class probability 0.984964
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2463570 120 + 27905053
UUCGCUCUGCGAUUUGCAUAUUUACGUGAAAGGGAGCGGGAGCUGAAAAACAAUAUCAUCCCGCGGCAGCACAAAAAAUGUAUGAAUUCCUAGGUCCACCUGGGAUGUUCAGAAAUUAAU
((((((((((..((..(........)..)).((((((....))(((.........))))))))))).)))............((((((((((((....))))))).))))))))...... ( -35.70)
>DroSec_CAF1 22544 114 + 1
UUCGCUCUGCGAUUUGCAUAUUUACGUGAAAGGGA------GCUGGAAAACAAUAUCAUCCCGCGGCAGCGCAAAAAAUGUAUGAAUUCCUAGGUCCACCUGGGAUGUUCAGAAAUUAAU
..((((((((..((..(........)..)).((((------....((........)).)))))))).)))).....(((...((((((((((((....))))))).)))))...)))... ( -34.20)
>DroSim_CAF1 19284 114 + 1
UUCGCUCUGCGAUUUGCAUAUUUACGUGGAAGGGA------GCUGGAAAACAAUAUCAUCCCGCGGCAGCGCAAAAAAUGUAUAAAUUCCUAGGUCCACCUGGGAUGUUCAGAAAUUAAU
..((((((((..((..(........)..)).((((------....((........)).)))))))).))))................(((((((....)))))))............... ( -30.00)
>DroEre_CAF1 23988 113 + 1
UUCGCUCUGCGAUUUGCAUAUUUACGUGAAAGGGA------GCUGAAAAACAAAAUCAUCCCGCAGCAGCG-AAAAAACGUAUGAAUUCCUAGGUCCACCUGGGAUGUUCAGAAAUUAAU
((((((((((..((..(........)..)).((((------..(((.........))))))))))).))))-))........((((((((((((....))))))).)))))......... ( -36.60)
>consensus
UUCGCUCUGCGAUUUGCAUAUUUACGUGAAAGGGA______GCUGAAAAACAAUAUCAUCCCGCGGCAGCGCAAAAAAUGUAUGAAUUCCUAGGUCCACCUGGGAUGUUCAGAAAUUAAU
((((((((((..((..(........)..)).((((........((.....))......)))))))).)))............((((((((((((....))))))).))))))))...... (-31.26 = -31.14 +  -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 09:49:27 2006