Locus 207

Sequence ID 3R_DroMel_CAF1
Location 869,229 – 869,653
Length 424
Max. P 0.995236
window362 window363 window364 window365 window366 window367 window368

overview

Window 2

Location 869,229 – 869,349
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.99
Mean single sequence MFE -35.58
Consensus MFE -31.17
Energy contribution -31.93
Covariance contribution 0.75
Combinations/Pair 1.11
Mean z-score -1.48
Structure conservation index 0.88
SVM decision value 0.29
SVM RNA-class probability 0.671118
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 869229 120 + 27905053
UUUAGCUACAGAUAUGGCCCAGCAGUCGGCCCAUAAGUCGCGUUAUUUGUAUUUGUGCCAGUAUCUGUGGCCGUAUCCGCAUCCGCAUCCGUAGCUGUAGCUGUAGCUGUAUCUGUAUCU
..(((((((.((((((((((((..(..(((..((((((.(((.....))))))))))))..)..))).))))))))).((....))....)))))))((((....))))........... ( -39.10)
>DroSec_CAF1 44251 113 + 1
UUUACCUACAGAUAUGGCCCAGAAGUCGGCCCAUAAGUCGCGUUAUUUGUAUUUGUGCCAGUAUCUGUGGCCGUAUCCGC------AUCCGUAGCUGUGGCUCUAGCUGUAUCUGUAUC-
......(((((((((((((((((.(..(((..((((((.(((.....))))))))))))..).)))).))))....((((------(........)))))........)))))))))..- ( -35.80)
>DroSim_CAF1 43456 113 + 1
UUUAGCUACAGAUAUGGCCCAGAAGUCGGUCCAUAAGUCGCGUUAUUUGUAUUUGUGCCAGUAUCCGUGGCCGUAUCCGC------AUCCGUAGCUGUAGCUCUAGCUGUAUCUGUAUC-
..(((((((.((((((((((.((.(..((..(((((((.(((.....))))))))))))..).)).).))))))))).(.------...))))))))((((....))))..........- ( -32.70)
>DroEre_CAF1 43469 113 + 1
UCUAGCUACAGAUAUGACCCAGAAGACGGCCCAUAAGUCGCGUUAUUUGUGCUUGUGCCAGUAUCUGUGGCUGUAUCCGU------AUCCGUAGCUGAAGCUGUAGCUGUAGCCGUAUC-
....(((((((((((..((((((..(((((..(((((.((((.....)))))))))))).)).)))).))..)))))...------..(..((((....))))..).))))))......- ( -34.70)
>consensus
UUUAGCUACAGAUAUGGCCCAGAAGUCGGCCCAUAAGUCGCGUUAUUUGUAUUUGUGCCAGUAUCUGUGGCCGUAUCCGC______AUCCGUAGCUGUAGCUCUAGCUGUAUCUGUAUC_
..(((((((((((((((((((((.(..(((..((((((.(((.....))))))))))))..).)))).)))))))))................((....))))))))))........... (-31.17 = -31.93 +   0.75)

alignment

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Window 3

Location 869,229 – 869,349
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.99
Mean single sequence MFE -32.84
Consensus MFE -27.14
Energy contribution -27.57
Covariance contribution 0.44
Combinations/Pair 1.11
Mean z-score -1.48
Structure conservation index 0.83
SVM decision value 0.14
SVM RNA-class probability 0.602241
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 869229 120 - 27905053
AGAUACAGAUACAGCUACAGCUACAGCUACGGAUGCGGAUGCGGAUACGGCCACAGAUACUGGCACAAAUACAAAUAACGCGACUUAUGGGCCGACUGCUGGGCCAUAUCUGUAGCUAAA
............(((....)))..(((((((((((.((..((((...(((((.((.....(.((...............)).)....))))))).))))....)).)))))))))))... ( -36.66)
>DroSec_CAF1 44251 113 - 1
-GAUACAGAUACAGCUAGAGCCACAGCUACGGAU------GCGGAUACGGCCACAGAUACUGGCACAAAUACAAAUAACGCGACUUAUGGGCCGACUUCUGGGCCAUAUCUGUAGGUAAA
-..((((((((.........((.((.(....).)------).))....((((.((((...((((.((....................)).))))...)))))))).))))))))...... ( -31.75)
>DroSim_CAF1 43456 113 - 1
-GAUACAGAUACAGCUAGAGCUACAGCUACGGAU------GCGGAUACGGCCACGGAUACUGGCACAAAUACAAAUAACGCGACUUAUGGACCGACUUCUGGGCCAUAUCUGUAGCUAAA
-...........(((....)))..((((((((((------(.(....)((((.((((...(((..((....................))..)))...)))))))).)))))))))))... ( -31.55)
>DroEre_CAF1 43469 113 - 1
-GAUACGGCUACAGCUACAGCUUCAGCUACGGAU------ACGGAUACAGCCACAGAUACUGGCACAAGCACAAAUAACGCGACUUAUGGGCCGUCUUCUGGGUCAUAUCUGUAGCUAGA
-.....((((..(((....)))..))))..((.(------(((((((..(((.((((...((((..((((.(.......).).)))....))))...)))))))..)))))))).))... ( -31.40)
>consensus
_GAUACAGAUACAGCUACAGCUACAGCUACGGAU______GCGGAUACGGCCACAGAUACUGGCACAAAUACAAAUAACGCGACUUAUGGGCCGACUUCUGGGCCAUAUCUGUAGCUAAA
............((((..(((....)))............(((((((.((((.((((...((((.((....................)).))))...)))))))).)))))))))))... (-27.14 = -27.57 +   0.44)

alignment

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secondary structure

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Window 4

Location 869,349 – 869,463
Length 114
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.11
Mean single sequence MFE -32.88
Consensus MFE -30.67
Energy contribution -30.30
Covariance contribution -0.37
Combinations/Pair 1.07
Mean z-score -1.43
Structure conservation index 0.93
SVM decision value 0.40
SVM RNA-class probability 0.719251
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 869349 114 - 27905053
AGCCUUGGAUUAGUCGCAGUCAGCUGCAUCUGACGGAUGCAGAUACUCGCACU------CGCACUCCCUUUUGUGCAAGCACCAAAAAAAAACUGGCACAAAUGUCACGCAGCCAUAUAC
.((.((((...(((.(((((...(((((((.....)))))))..))).)))))------.((((........)))).....))))........(((((....))))).)).......... ( -30.30)
>DroSec_CAF1 44364 108 - 1
UGCCUUGGAUUAGUCGCAGUCAGCUGCAUCUGACGGAUGCAGAUACUCGCACU------CGCACUCGCUGUUGUGCAAGAACCGAAA-AAAACUGGCACAAAUGUCACGCAGCCA-----
(((.((((.......(((((...(((((((.....)))))))..))).)).((------.((((........)))).))..))))..-.....(((((....))))).)))....----- ( -30.70)
>DroSim_CAF1 43569 108 - 1
GGCCUCGGAUUAGUCGCAGUCAGCUGCAUCUGACGGAUGCAGAUACUCGCACU------UGCACUCGCUGUUGUGCAAGAACCGAAA-AAAACUGGCACAAAUGUCACGCAGCCA-----
(((.((((.......(((((...(((((((.....)))))))..))).)).((------(((((........)))))))..))))..-.....(((((....)))))....))).----- ( -39.40)
>DroEre_CAF1 43582 115 - 1
UGCCUUGGAUUAGUCGCAGUCAGCUGCAUCUGACGGAUGCAGAUACUCGCACUCGCACUCGCACUCGCUGUUGUGCAAGCACCGAAAAAAAACUGGCACAAAUGUCACGCAGCCA-----
(((.((((...(((.(((((...(((((((.....)))))))..))).))))).((((..((....))....)))).....))))........(((((....))))).)))....----- ( -31.10)
>consensus
UGCCUUGGAUUAGUCGCAGUCAGCUGCAUCUGACGGAUGCAGAUACUCGCACU______CGCACUCGCUGUUGUGCAAGAACCGAAA_AAAACUGGCACAAAUGUCACGCAGCCA_____
.((.((((...(((.(((((...(((((((.....)))))))..))).))))).......((((........)))).....))))........(((((....))))).)).......... (-30.67 = -30.30 +  -0.37)

alignment

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secondary structure

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Window 5

Location 869,463 – 869,583
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -26.22
Consensus MFE -20.73
Energy contribution -21.35
Covariance contribution 0.62
Combinations/Pair 1.03
Mean z-score -2.00
Structure conservation index 0.79
SVM decision value 0.35
SVM RNA-class probability 0.700813
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 869463 120 + 27905053
GAAUUCGGCGGGGUUCCUGGCUUACACUCAGCCACUUCGCAUUUUAAUUAAAACGAAUUGCGCAUUAUUUGCGCCUGGCGUUAUAAUUUAAUUAAUAAGCCUUAAUUAAAACCUAAUAAG
.......(((((((....((((.......))))))))))).((((((((((........(((((.....)))))..(((.((((..........)))))))))))))))))......... ( -29.00)
>DroSec_CAF1 44472 120 + 1
CAAUUCGGCGGGGUUCCUGCCUUACACUCAGCCACUUCGCAUUUUAAUUAAAACGAAUCGCGUAUUAUUUACGCCUGGCGUUAUAAUUUAAUUAAUAAGCCUUAAUUAAAACCUAAUUAG
......((((((...)))))).........((((.((((..((......))..))))..(((((.....))))).)))).......(((((((((......))))))))).......... ( -25.40)
>DroSim_CAF1 43677 120 + 1
CAAUUCGGCGGGGUUCCUGCCUUACACUCAGCCACUUCGCAUUUUAAUUAAAACGAAUCGCGUAUUAUUUACGCCUGGCGUUAUAAUUUAAUUAAUAAGCCUUAAUUAAAACCUAAUUAG
......((((((...)))))).........((((.((((..((......))..))))..(((((.....))))).)))).......(((((((((......))))))))).......... ( -25.40)
>DroEre_CAF1 43697 120 + 1
CCAUUCAGGGGGGGUCCUACCUUACAUUCCGCCACUUCGCAUUUUAAUUAAAACGAAUCGCGUAUUAUUUACGCCUGGCGUUUUAAUUUAAUUAAUAAGCCCUAAUUAAAACUUAAUUAG
.......((.(((((..........))))).)).(((........((((((((((....(((((.....)))))....))))))))))........)))..(((((((.....))))))) ( -25.09)
>consensus
CAAUUCGGCGGGGUUCCUGCCUUACACUCAGCCACUUCGCAUUUUAAUUAAAACGAAUCGCGUAUUAUUUACGCCUGGCGUUAUAAUUUAAUUAAUAAGCCUUAAUUAAAACCUAAUUAG
......((((((...)))))).........((((.((((..((......))..))))..(((((.....))))).)))).......(((((((((......))))))))).......... (-20.73 = -21.35 +   0.62)

alignment

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secondary structure

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Window 6

Location 869,503 – 869,619
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.34
Mean single sequence MFE -28.13
Consensus MFE -27.89
Energy contribution -27.32
Covariance contribution -0.56
Combinations/Pair 1.06
Mean z-score -2.88
Structure conservation index 0.99
SVM decision value 2.55
SVM RNA-class probability 0.995236
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 869503 116 + 27905053
AUUUUAAUUAAAACGAAUUGCGCAUUAUUUGCGCCUGGCGUUAUAAUUUAAUUAAUAAGCCUUAAUUAAAACCUAAUAAGGUUUUAAUUGUAUUGUGUUGCAUGUGGCAAAGACAU----
...((((((((((((....(((((.....)))))....))).....)))))))))...(((..(((((((((((....)))))))))))(((......)))....)))........---- ( -29.60)
>DroSec_CAF1 44512 120 + 1
AUUUUAAUUAAAACGAAUCGCGUAUUAUUUACGCCUGGCGUUAUAAUUUAAUUAAUAAGCCUUAAUUAAAACCUAAUUAGGUUUUAAUUGUAUUGUGUUGCAUGUGGCAAAGACAUUCCG
...((((((((((((....(((((.....)))))....))).....)))))))))...(((..(((((((((((....)))))))))))(((......)))....)))............ ( -27.60)
>DroSim_CAF1 43717 116 + 1
AUUUUAAUUAAAACGAAUCGCGUAUUAUUUACGCCUGGCGUUAUAAUUUAAUUAAUAAGCCUUAAUUAAAACCUAAUUAGGUUUUAAUUGUAUUGUGUUGCAUGUGGCAAAGACAU----
...((((((((((((....(((((.....)))))....))).....)))))))))...(((..(((((((((((....)))))))))))(((......)))....)))........---- ( -27.60)
>DroEre_CAF1 43737 116 + 1
AUUUUAAUUAAAACGAAUCGCGUAUUAUUUACGCCUGGCGUUUUAAUUUAAUUAAUAAGCCCUAAUUAAAACUUAAUUAGGUUUUAAUUGUAUUGUGUUGCAUGUGGCAAAGACAU----
.....((((((((((....(((((.....)))))....))))))))))..........(((..(((((((((((....)))))))))))(((......)))....)))........---- ( -27.70)
>consensus
AUUUUAAUUAAAACGAAUCGCGUAUUAUUUACGCCUGGCGUUAUAAUUUAAUUAAUAAGCCUUAAUUAAAACCUAAUUAGGUUUUAAUUGUAUUGUGUUGCAUGUGGCAAAGACAU____
...((((((((((((....(((((.....)))))....))).....)))))))))...(((..(((((((((((....)))))))))))(((......)))....)))............ (-27.89 = -27.32 +  -0.56)

alignment

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secondary structure

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Window 7

Location 869,503 – 869,619
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.34
Mean single sequence MFE -25.67
Consensus MFE -24.59
Energy contribution -24.28
Covariance contribution -0.31
Combinations/Pair 1.06
Mean z-score -3.53
Structure conservation index 0.96
SVM decision value 2.39
SVM RNA-class probability 0.993281
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 869503 116 - 27905053
----AUGUCUUUGCCACAUGCAACACAAUACAAUUAAAACCUUAUUAGGUUUUAAUUAAGGCUUAUUAAUUAAAUUAUAACGCCAGGCGCAAAUAAUGCGCAAUUCGUUUUAAUUAAAAU
----..((((((((.....))).........(((((((((((....))))))))))))))))..........(((((.((((....(((((.....)))))....)))).)))))..... ( -28.30)
>DroSec_CAF1 44512 120 - 1
CGGAAUGUCUUUGCCACAUGCAACACAAUACAAUUAAAACCUAAUUAGGUUUUAAUUAAGGCUUAUUAAUUAAAUUAUAACGCCAGGCGUAAAUAAUACGCGAUUCGUUUUAAUUAAAAU
......((((((((.....))).........(((((((((((....))))))))))))))))..........(((((.((((....(((((.....)))))....)))).)))))..... ( -24.90)
>DroSim_CAF1 43717 116 - 1
----AUGUCUUUGCCACAUGCAACACAAUACAAUUAAAACCUAAUUAGGUUUUAAUUAAGGCUUAUUAAUUAAAUUAUAACGCCAGGCGUAAAUAAUACGCGAUUCGUUUUAAUUAAAAU
----..((((((((.....))).........(((((((((((....))))))))))))))))..........(((((.((((....(((((.....)))))....)))).)))))..... ( -24.90)
>DroEre_CAF1 43737 116 - 1
----AUGUCUUUGCCACAUGCAACACAAUACAAUUAAAACCUAAUUAAGUUUUAAUUAGGGCUUAUUAAUUAAAUUAAAACGCCAGGCGUAAAUAAUACGCGAUUCGUUUUAAUUAAAAU
----.(((..((((.....)))).))).......(((..((((((((.....))))))))..))).......((((((((((....(((((.....)))))....))))))))))..... ( -24.60)
>consensus
____AUGUCUUUGCCACAUGCAACACAAUACAAUUAAAACCUAAUUAGGUUUUAAUUAAGGCUUAUUAAUUAAAUUAUAACGCCAGGCGUAAAUAAUACGCGAUUCGUUUUAAUUAAAAU
......((((((((.....))).........(((((((((((....))))))))))))))))..........(((((.((((....(((((.....)))))....)))).)))))..... (-24.59 = -24.28 +  -0.31)

alignment

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secondary structure

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Window 8

Location 869,543 – 869,653
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.00
Mean single sequence MFE -21.55
Consensus MFE -17.10
Energy contribution -17.29
Covariance contribution 0.19
Combinations/Pair 1.07
Mean z-score -1.71
Structure conservation index 0.79
SVM decision value 0.40
SVM RNA-class probability 0.720295
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 869543 110 - 27905053
CCGCUGUUACAAAACAUACUUUCAGACGGGCGGA----------AUGUCUUUGCCACAUGCAACACAAUACAAUUAAAACCUUAUUAGGUUUUAAUUAAGGCUUAUUAAUUAAAUUAUAA
((((((((..(((......)))..))).))))).----------..((((((((.....))).........(((((((((((....)))))))))))))))).................. ( -21.70)
>DroSec_CAF1 44552 120 - 1
CCGCUGUUACACAACAUACUUUCAGACGGGCGGAAUGUCGCGGAAUGUCUUUGCCACAUGCAACACAAUACAAUUAAAACCUAAUUAGGUUUUAAUUAAGGCUUAUUAAUUAAAUUAUAA
((((((((....))))........((((.......))))))))...((((((((.....))).........(((((((((((....)))))))))))))))).................. ( -24.60)
>DroSim_CAF1 43757 110 - 1
CCGCUGUUACACAACAUACUUUCAGACGGGCGGA----------AUGUCUUUGCCACAUGCAACACAAUACAAUUAAAACCUAAUUAGGUUUUAAUUAAGGCUUAUUAAUUAAAUUAUAA
((((((((................))).))))).----------..((((((((.....))).........(((((((((((....)))))))))))))))).................. ( -21.39)
>DroEre_CAF1 43777 110 - 1
CCAGUGUAGCGCAAUAUAUUUUCAGACGGUCGGA----------AUGUCUUUGCCACAUGCAACACAAUACAAUUAAAACCUAAUUAAGUUUUAAUUAGGGCUUAUUAAUUAAAUUAAAA
...((((.((((((.........(((((......----------.))))))))).....)).))))........(((..((((((((.....))))))))..)))............... ( -18.50)
>consensus
CCGCUGUUACACAACAUACUUUCAGACGGGCGGA__________AUGUCUUUGCCACAUGCAACACAAUACAAUUAAAACCUAAUUAGGUUUUAAUUAAGGCUUAUUAAUUAAAUUAUAA
((((((((................))).))))).............((((((((.....))).........(((((((((((....)))))))))))))))).................. (-17.10 = -17.29 +   0.19)

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 09:37:32 2006