Locus 1555

Sequence ID X_DroMel_CAF1
Location 4,465,255 – 4,465,517
Length 262
Max. P 0.984353
window2553 window2554 window2555 window2556 window2557

overview

Window 3

Location 4,465,255 – 4,465,375
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.03
Mean single sequence MFE -52.60
Consensus MFE -45.17
Energy contribution -45.55
Covariance contribution 0.38
Combinations/Pair 1.11
Mean z-score -3.12
Structure conservation index 0.86
SVM decision value 1.69
SVM RNA-class probability 0.972259
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4465255 120 + 22224390
ACAACAGCACAGUGGAAUCGGAAAUGGAGCGCCAGCGACGGGACUCCACCACAUCGGAGUCCUCGCUGGAGCAUCUGGAUCUGGGACGUACGCCCAAAAAACUGGGCGGUAACAGUGGCU
.....(((.((.(((..(((((..((((((.(((((((..(((((((........)))))))))))))).)).))))..)))))..)...((((((......))))))....)).))))) ( -54.70)
>DroSec_CAF1 66906 120 + 1
ACAACAGCACAGUGGAAUCGGAAAUGGAGCGCCAGCGACGUGACUCCACCACAUCGGAGUCCUCGCUGGAGCAUCUGGAUCUGGGCCGUACGCCCAAAAAACUGGGCGGCAACAGUGGCU
.....(((.((.(((..(((((..((((((.(((((((.(.((((((........)))))))))))))).)).))))..)))))..)((.((((((......))))))))..)).))))) ( -53.20)
>DroEre_CAF1 70648 120 + 1
ACAACAGCACAGCGGAAUCCGAAAUGGAGCGCCAGCGGCGGGACUCCACCACAUCGGAGUCCUCCCUGGAGCAUCUGGAUCUGGGACGUACGCCCAAGAAACUGGGCGGCAACAGUGGCU
.......(((.(((...(((((..((((((.((((.((.((((((((........)))))))))))))).)).))))..)).))).))).((((((......))))))......)))... ( -49.60)
>DroYak_CAF1 67800 120 + 1
ACAACAGCACAGCGGAGUCGGAAAUGGAGCGUCAGCGGCGGGACUCGACCACAUCGGAGUCCUCGCUGGAGCACCUGGAUCUGGGCCGCACGCCCAAGAAACUGGGCGGCAACAGUGGCU
.......(((.((((..(((((...((.((..(((((..(((((((((.....)).))))))))))))..)).))....))))).)))).((((((......))))))......)))... ( -52.90)
>consensus
ACAACAGCACAGCGGAAUCGGAAAUGGAGCGCCAGCGACGGGACUCCACCACAUCGGAGUCCUCGCUGGAGCAUCUGGAUCUGGGACGUACGCCCAAAAAACUGGGCGGCAACAGUGGCU
.......(((.(((...(((((..((((((.(((((((..(((((((........)))))))))))))).)).))))..)))))..))).((((((......))))))......)))... (-45.17 = -45.55 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 4,465,295 – 4,465,397
Length 102
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 94.12
Mean single sequence MFE -39.90
Consensus MFE -36.39
Energy contribution -36.32
Covariance contribution -0.06
Combinations/Pair 1.13
Mean z-score -2.59
Structure conservation index 0.91
SVM decision value 1.97
SVM RNA-class probability 0.984353
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4465295 102 + 22224390
GGACUCCACCACAUCGGAGUCCUCGCUGGAGCAUCUGGAUCUGGGACGUACGCCCAAAAAACUGGGCGGUAACAGUGGCUCUACACAGACCACAUCCACGCC
(((((((........)))))))..((((((.....(((.((((....((.((((((......))))))...)).(((....))).)))))))..)))).)). ( -39.10)
>DroSec_CAF1 66946 102 + 1
UGACUCCACCACAUCGGAGUCCUCGCUGGAGCAUCUGGAUCUGGGCCGUACGCCCAAAAAACUGGGCGGCAACAGUGGCUCUACACAGACCACAUCCACGCC
.((((((........))))))...((((((...((((.....((((((...(((((......)))))(....)..))))))....)))).....)))).)). ( -39.50)
>DroEre_CAF1 70688 102 + 1
GGACUCCACCACAUCGGAGUCCUCCCUGGAGCAUCUGGAUCUGGGACGUACGCCCAAGAAACUGGGCGGCAACAGUGGCUCCGCGCAGACCACAUCCACGCC
(((((((........)))))))....((((.....(((.((((....((.((((((......))))))))....(((....))).)))))))..)))).... ( -38.90)
>DroYak_CAF1 67840 102 + 1
GGACUCGACCACAUCGGAGUCCUCGCUGGAGCACCUGGAUCUGGGCCGCACGCCCAAGAAACUGGGCGGCAACAGUGGCUCCACACAGACCACAUCCACGCC
((((((((.....)).))))))..((((((.....(((.((((((((((..(((((......)))))(....).)))))).....)))))))..)))).)). ( -42.10)
>consensus
GGACUCCACCACAUCGGAGUCCUCGCUGGAGCAUCUGGAUCUGGGACGUACGCCCAAAAAACUGGGCGGCAACAGUGGCUCCACACAGACCACAUCCACGCC
(((((((........)))))))..((((((.....(((.((((....((.((((((......))))))))....(((....))).)))))))..)))).)). (-36.39 = -36.32 +  -0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 4,465,335 – 4,465,437
Length 102
Sequences 4
Columns 102
Reading direction forward
Mean pairwise identity 91.01
Mean single sequence MFE -39.35
Consensus MFE -33.74
Energy contribution -36.30
Covariance contribution 2.56
Combinations/Pair 1.04
Mean z-score -2.10
Structure conservation index 0.86
SVM decision value 1.26
SVM RNA-class probability 0.937142
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4465335 102 + 22224390
CUGGGACGUACGCCCAAAAAACUGGGCGGUAACAGUGGCUCUACACAGACCACAUCCACGCCACAUGAGCUGGCUACGGUGACAUCUUCGCGCAAGCGCAAA
...(((.((.((((((......))))))...)).((((.(((....))))))).)))..((((.......))))...(....).....(((....))).... ( -34.00)
>DroSec_CAF1 66986 102 + 1
CUGGGCCGUACGCCCAAAAAACUGGGCGGCAACAGUGGCUCUACACAGACCACAUCCACGCCACAUGAGCUGACUACGGUGACGUCGUCGCGCAAGCGUAAG
.(((((.((.((((((......))))))))....((((.(((....)))))))......))).))......(((.(((....))).)))((....))..... ( -38.50)
>DroEre_CAF1 70728 102 + 1
CUGGGACGUACGCCCAAGAAACUGGGCGGCAACAGUGGCUCCGCGCAGACCACAUCCACGCCACAUGAGUCGACGACGGUGGCGUCGUCGCGCAAGCGUAAA
...(((.((.((((((......))))))))....((((((......)).)))).)))(((((((....(((...))).)))))))...(((....))).... ( -40.20)
>DroYak_CAF1 67880 102 + 1
CUGGGCCGCACGCCCAAGAAACUGGGCGGCAACAGUGGCUCCACACAGACCACAUCCACGCCACAUGAGGUGACGACGGUGGCGUCGUCGCGCAAGCGUAAA
.((((((((..(((((......)))))(....).))))).)))..............(((((((....(....)....)))))))...(((....))).... ( -44.70)
>consensus
CUGGGACGUACGCCCAAAAAACUGGGCGGCAACAGUGGCUCCACACAGACCACAUCCACGCCACAUGAGCUGACGACGGUGACGUCGUCGCGCAAGCGUAAA
.((((.(((.((((((......))))))......((((.((......))))))....))))).))......(((((((....)))))))((....))..... (-33.74 = -36.30 +   2.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 4,465,397 – 4,465,517
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 80.83
Mean single sequence MFE -40.93
Consensus MFE -25.21
Energy contribution -25.43
Covariance contribution 0.23
Combinations/Pair 1.09
Mean z-score -1.99
Structure conservation index 0.62
SVM decision value 0.22
SVM RNA-class probability 0.639858
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4465397 120 + 22224390
ACAUGAGCUGGCUACGGUGACAUCUUCGCGCAAGCGCAAAAUUCGCCAUUUGCAAUUGAAUCACCAUCAGCAGCAGCAGCAUCACCAGCAGUCGGAUCUGCUGAGUGAUGAAGACGUGGC
.((((.(((((((..(((((....(((((....))(((((........)))))....))))))))...)))..))))..((((((((((((......)))))).))))))....)))).. ( -46.30)
>DroSec_CAF1 67048 116 + 1
ACAUGAGCUGACUACGGUGACGUCGUCGCGCAAGCGUAAGCUUCGCCAUUUGCAAUUGAAUCACCAUCAGCAGCAGCAGCAUCAUCAGCAGUCGGAUCUGCUGAGUGAUGAGGACG----
....((((((((.(((....))).)))((....))...)))))((((..((((..((((.......))))..))))...((((((((((((......))))))).))))).)).))---- ( -42.50)
>DroYak_CAF1 67942 108 + 1
ACAUGAGGUGACGACGGUGGCGUCGUCGCGCAAGCGUAAACUUCGCCACUUGCAACUGAAUCACCACCAACAGCAG------------CACUCGGAACUGCUGAGCGAUGAGGACGAGUC
....((((((((((((....)))))))((....))....)))))(((.(((((...((......))....((((((------------.........)))))).)))).).)).)..... ( -34.00)
>consensus
ACAUGAGCUGACUACGGUGACGUCGUCGCGCAAGCGUAAACUUCGCCAUUUGCAAUUGAAUCACCAUCAGCAGCAGCAGCAUCA_CAGCAGUCGGAUCUGCUGAGUGAUGAGGACG_G_C
...............(((((.((...(((....)))...)).))))).............((..((((..((((((.....................))))))...))))..))...... (-25.21 = -25.43 +   0.23)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 4,465,397 – 4,465,517
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.83
Mean single sequence MFE -43.17
Consensus MFE -24.81
Energy contribution -23.93
Covariance contribution -0.88
Combinations/Pair 1.16
Mean z-score -2.13
Structure conservation index 0.57
SVM decision value -0.04
SVM RNA-class probability 0.511568
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4465397 120 - 22224390
GCCACGUCUUCAUCACUCAGCAGAUCCGACUGCUGGUGAUGCUGCUGCUGCUGAUGGUGAUUCAAUUGCAAAUGGCGAAUUUUGCGCUUGCGCGAAGAUGUCACCGUAGCCAGCUCAUGU
...((((...((((((.((((((......))))))))))))..((((..(((.((((((((((..((((.....))))..((((((....)))))))).)))))))))))))))..)))) ( -46.40)
>DroSec_CAF1 67048 116 - 1
----CGUCCUCAUCACUCAGCAGAUCCGACUGCUGAUGAUGCUGCUGCUGCUGAUGGUGAUUCAAUUGCAAAUGGCGAAGCUUACGCUUGCGCGACGACGUCACCGUAGUCAGCUCAUGU
----.((...(((((.(((((((......))))))))))))..)).((((((.((((((((....((((....((((.......))))...))))....)))))))))).))))...... ( -40.90)
>DroYak_CAF1 67942 108 - 1
GACUCGUCCUCAUCGCUCAGCAGUUCCGAGUG------------CUGCUGUUGGUGGUGAUUCAGUUGCAAGUGGCGAAGUUUACGCUUGCGCGACGACGCCACCGUCGUCACCUCAUGU
((((.(...(((((((((((((((.......)------------))))))..))))))))..)))))(((((((..........)))))))..(((((((....)))))))......... ( -42.20)
>consensus
G_C_CGUCCUCAUCACUCAGCAGAUCCGACUGCUG_UGAUGCUGCUGCUGCUGAUGGUGAUUCAAUUGCAAAUGGCGAAGUUUACGCUUGCGCGACGACGUCACCGUAGUCAGCUCAUGU
....((((.((((((.(((((((........................))))))))))))).....((((....((((.......))))...)))).)))).................... (-24.81 = -23.93 +  -0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:24 2006