Locus 4677

Sequence ID 2L_DroMel_CAF1
Location 13,440,676 – 13,440,801
Length 125
Max. P 0.997079
window7392 window7393 window7394

overview

Window 2

Location 13,440,676 – 13,440,770
Length 94
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 81.13
Mean single sequence MFE -22.47
Consensus MFE -15.60
Energy contribution -17.18
Covariance contribution 1.58
Combinations/Pair 1.10
Mean z-score -1.24
Structure conservation index 0.69
SVM decision value -0.04
SVM RNA-class probability 0.514355
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13440676 94 - 22407834
UUGUGGGUGGUGGGUGGACAAAAGGUCACGCAAUCGUGCGGCAAAAAAAAAAAAGGGCUGACAGUGUAGGGAGCGCAAGUUGGCCAAAUGUUUU
((((.((((((..((((((.....))).))).))))).).))))...........(((..((.((((.....))))..))..)))......... ( -23.10)
>DroVir_CAF1 83664 81 - 1
AUG---AAAGUUGAUGCCCAAAAGGCCAAGCAAUUGU--AGCCA-------AAAGGGCUGACAGCAUAA-AAGCGAGACUUGGCAAAAUUACAU
...---..................(((((((...(((--((((.-------....)))).)))((....-..))..).)))))).......... ( -18.70)
>DroSec_CAF1 47586 92 - 1
UUGUGGGUGGUGGGUGGACAAAAGGCCACGCAAUCGUGCGGCAAAAA--AAAAAGGGCUGACAGUGUAGGGAGCGCAAGUUGGCCAAAUGUUUU
.((((.(...((.((((........)))).))..).)))).......--......(((..((.((((.....))))..))..)))......... ( -24.00)
>DroSim_CAF1 48744 91 - 1
UUGUGGGUGGUGGGUGGACAAAAGGCCACGCAAUCGUGCGGCAAAAA---AAAAGGGCUGACAGUGUAGGGAGCGCAAGUUGGCCAAAUGUUUU
.((((.(...((.((((........)))).))..).)))).......---.....(((..((.((((.....))))..))..)))......... ( -24.00)
>DroEre_CAF1 52014 82 - 1
UGGUGGGU-------GGACAAAAGGCCACGCAAUCGUGCGGCAGAA-----AAAGGGCUGACAGUGUAUGGCGCGCAAGUUGGCCAAAUGUUUU
........-------(((((....(((.(((....))).)))....-----....(((..((.((((.....))))..))..)))...))))). ( -23.30)
>DroYak_CAF1 48341 89 - 1
UUGUGGGUGGUGGGAGGACAAAAGGCCACGCAAUCGUGCGGCAAAA-----AAAGGGCUGACAGAGUAGGGAGCGCAAGUUGGCCAAAUGUUUU
..............((((((...(((((((((....))))......-----...(.(((..(......)..))).)....)))))...)))))) ( -21.70)
>consensus
UUGUGGGUGGUGGGUGGACAAAAGGCCACGCAAUCGUGCGGCAAAA_____AAAGGGCUGACAGUGUAGGGAGCGCAAGUUGGCCAAAUGUUUU
...............(((((....(((.(((....))).))).............(((..((.((((.....))))..))..)))...))))). (-15.60 = -17.18 +   1.58)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 13,440,700 – 13,440,801
Length 101
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 75.37
Mean single sequence MFE -32.48
Consensus MFE -16.54
Energy contribution -18.32
Covariance contribution 1.78
Combinations/Pair 1.17
Mean z-score -2.25
Structure conservation index 0.51
SVM decision value 1.41
SVM RNA-class probability 0.951242
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13440700 101 + 22407834
CCUACACUGUCAGCCCUUUUUUUUUUUUGCCGCACGAUUGCGUGACCUUUUGUCCACCCACCACCCACAAGCCACCAUCAAAGUGGGUGG-------UUUGGUUGG-UU
........((((((..............))((((....)))))))).......(((.(((((((((((..............))))))))-------)..)).)))-.. ( -25.48)
>DroVir_CAF1 83688 81 + 1
-UUAUGCUGUCAGCCCUUU-------UGGCU--ACAAUUGCUUGGCCUUUUGGGCAUCAACUUU---CAUUG-------AAAGUGUGUGU-------G-UGUGUGAGAG
-((((((...((((((...-------.((((--(........)))))....))))....(((((---(...)-------)))))...)).-------.-.))))))... ( -22.30)
>DroSec_CAF1 47610 99 + 1
CCUACACUGUCAGCCCUUUUU--UUUUUGCCGCACGAUUGCGUGGCCUUUUGUCCACCCACCACCCACAAGCCACCAUCAAAGUGGGUGG-------GUUGGGUGG-UU
.....................--.....(((((........))))).......(((((((((((((((..............))))))))-------..)))))))-.. ( -34.14)
>DroSim_CAF1 48768 98 + 1
CCUACACUGUCAGCCCUUUU---UUUUUGCCGCACGAUUGCGUGGCCUUUUGUCCACCCACCACCCACAAGCCACCAUCAAAGUGGGUGG-------GUUGGGUGG-UC
....................---.....(((((........))))).......(((((((((((((((..............))))))))-------..)))))))-.. ( -34.14)
>DroEre_CAF1 52038 95 + 1
CAUACACUGUCAGCCCUUU-----UUCUGCCGCACGAUUGCGUGGCCUUUUGUCC-------ACCCACCAGCCACCUUCAAUGUGGGCGGU-GGGUGGUUGGGUGG-UG
....((((....((((...-----....(((((........))))).......((-------(((((((.(((..(......)..))))))-))))))..))))))-)) ( -39.50)
>DroYak_CAF1 48365 103 + 1
CCUACUCUGUCAGCCCUUU-----UUUUGCCGCACGAUUGCGUGGCCUUUUGUCCUCCCACCACCCACAAGCCACCAUCAAUGUGGGUGGUUGGGUGGUUGGGUGG-UU
.((((((............-----....(((((........))))).......((.(((((((((((((............))))))))).)))).))..))))))-.. ( -39.30)
>consensus
CCUACACUGUCAGCCCUUU_____UUUUGCCGCACGAUUGCGUGGCCUUUUGUCCACCCACCACCCACAAGCCACCAUCAAAGUGGGUGG_______GUUGGGUGG_UU
............((((............(((((.(....).)))))..............((((((((..............))))))))..........))))..... (-16.54 = -18.32 +   1.78)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,440,700 – 13,440,801
Length 101
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 75.37
Mean single sequence MFE -34.96
Consensus MFE -18.64
Energy contribution -20.56
Covariance contribution 1.92
Combinations/Pair 1.11
Mean z-score -3.10
Structure conservation index 0.53
SVM decision value 2.79
SVM RNA-class probability 0.997079
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13440700 101 - 22407834
AA-CCAACCAAA-------CCACCCACUUUGAUGGUGGCUUGUGGGUGGUGGGUGGACAAAAGGUCACGCAAUCGUGCGGCAAAAAAAAAAAAGGGCUGACAGUGUAGG
..-(((.((..(-------((((((((..............))))))))).)))))(((....((((((((....))))((..............))))))..)))... ( -31.18)
>DroVir_CAF1 83688 81 - 1
CUCUCACACA-C-------ACACACACUUU-------CAAUG---AAAGUUGAUGCCCAAAAGGCCAAGCAAUUGU--AGCCA-------AAAGGGCUGACAGCAUAA-
((.(((....-.-------..........(-------((((.---...))))).((((....((((((....))).--.))).-------...))))))).)).....- ( -17.90)
>DroSec_CAF1 47610 99 - 1
AA-CCACCCAAC-------CCACCCACUUUGAUGGUGGCUUGUGGGUGGUGGGUGGACAAAAGGCCACGCAAUCGUGCGGCAAAAA--AAAAAGGGCUGACAGUGUAGG
..-(((((((((-------(((((((((.....)))))...))))))..)))))))(((...((((.((((....)))).......--......)))).....)))... ( -39.04)
>DroSim_CAF1 48768 98 - 1
GA-CCACCCAAC-------CCACCCACUUUGAUGGUGGCUUGUGGGUGGUGGGUGGACAAAAGGCCACGCAAUCGUGCGGCAAAAA---AAAAGGGCUGACAGUGUAGG
..-(((((((((-------(((((((((.....)))))...))))))..)))))))(((...((((.((((....)))).......---.....)))).....)))... ( -39.12)
>DroEre_CAF1 52038 95 - 1
CA-CCACCCAACCACCC-ACCGCCCACAUUGAAGGUGGCUGGUGGGU-------GGACAAAAGGCCACGCAAUCGUGCGGCAGAA-----AAAGGGCUGACAGUGUAUG
((-((((((..((((((-((((.((((.......)))).))))))))-------)).......(((.(((....))).)))....-----...))).))...))).... ( -41.50)
>DroYak_CAF1 48365 103 - 1
AA-CCACCCAACCACCCAACCACCCACAUUGAUGGUGGCUUGUGGGUGGUGGGAGGACAAAAGGCCACGCAAUCGUGCGGCAAAA-----AAAGGGCUGACAGAGUAGG
..-.(((((..((.((((.(((((((((............))))))))))))).)).......(((.(((....))).)))....-----...))).)).......... ( -41.00)
>consensus
AA_CCACCCAAC_______CCACCCACUUUGAUGGUGGCUUGUGGGUGGUGGGUGGACAAAAGGCCACGCAAUCGUGCGGCAAAA_____AAAGGGCUGACAGUGUAGG
....(((((..........((((((((..............))))))))..............(((.(((....))).)))............))).)).......... (-18.64 = -20.56 +   1.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:22 2006