Locus 6304

Sequence ID 2R_DroMel_CAF1
Location 19,752,773 – 19,752,882
Length 109
Max. P 0.805409
window10075 window10076

overview

Window 5

Location 19,752,773 – 19,752,882
Length 109
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 81.69
Mean single sequence MFE -27.83
Consensus MFE -17.42
Energy contribution -18.53
Covariance contribution 1.11
Combinations/Pair 1.16
Mean z-score -2.41
Structure conservation index 0.63
SVM decision value 0.63
SVM RNA-class probability 0.805409
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19752773 109 + 20766785
GAAGCAAAGCCAGCAAAGGCUGGAGCAGGAGCAAAAAAUAAUUUAUAACCACGACGUGUGGCUGGCCAAACAAAAAA----CAUCCACAGCCAGAUUUUCUACGCUCCUG-C--UU
.........(((((....)))))(((((((((................((((.....))))(((((...........----........))))).........)))))))-)--). ( -36.31)
>DroPse_CAF1 13290 114 + 1
AAAGAAAAACCGAGCAAGAACCGAGCAGGGG--AAAAAUAAUUUAUAACCACGACGUGUGGCUGGCCCGAAAAAAAAAUUCAAACCAGAGCCAGAUUUUUUGUACUGUAGCCCAAU
........................(((((.(--((((((.........((((.....))))(((((.(...................).)))))))))))).).))))........ ( -18.21)
>DroSec_CAF1 5589 109 + 1
GAAGGAAAGCCAACAAAGGCGGGAGCAGGAGCAAAAAAUAAUUUAUAACCACGACGUGUGGCUGGCCAAACAAAAAA----CAUCCACAGCCAGAUUUUUUACGCUCCUC-C--CA
........(((......)))((((...((((((((((((.........((((.....))))(((((...........----........))))))))))))..)))))))-)--). ( -31.51)
>DroSim_CAF1 8610 109 + 1
UAAGGAAAGCCAACAAAGGCGGGAGCAGGAGCAAAAAAUAAUUUAUAACCACGACGUGUGGCUGGCCAAACAAAAAA----CAUCCACAGCCAGAUUUUUUACGCUCCUC-C--CA
........(((......)))((((...((((((((((((.........((((.....))))(((((...........----........))))))))))))..)))))))-)--). ( -31.51)
>DroEre_CAF1 5733 110 + 1
GAAGGAAAGCCGCCAGGAGCAGGAGCAGGAGCAAAAAAUAAUUUAUAACCACGACGUGUGGCUGGCCAAACAAAAAA---CCAUCCACGGCCAGAUUUUUUACGCUUCUC-C--AU
...(((..((..((.......)).)).((((((((((((.........((((.....))))((((((..........---........)))))))))))))..)))))))-)--.. ( -27.87)
>DroYak_CAF1 8541 104 + 1
GAAGGAGAGCAGCCAGGAGC------AGAAGCAAAAAAUAAUUUAUAACCACGACGUGUGGCUGCCCAAACAAAAAA---CCAUCCACAGCCAGAUUUUUUACGCUUCUC-C--AU
...((((((((((((...((------....)).................(((...))))))))))............---........(((............)))))))-)--.. ( -21.60)
>consensus
GAAGGAAAGCCAACAAAGGCGGGAGCAGGAGCAAAAAAUAAUUUAUAACCACGACGUGUGGCUGGCCAAACAAAAAA____CAUCCACAGCCAGAUUUUUUACGCUCCUC_C__AU
........(((......)))......(((((((((((((.........((((.....))))(((((.......................))))))))))))..))))))....... (-17.42 = -18.53 +   1.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 19,752,773 – 19,752,882
Length 109
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 81.69
Mean single sequence MFE -32.77
Consensus MFE -20.61
Energy contribution -21.31
Covariance contribution 0.70
Combinations/Pair 1.24
Mean z-score -2.17
Structure conservation index 0.63
SVM decision value 0.46
SVM RNA-class probability 0.745101
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19752773 109 - 20766785
AA--G-CAGGAGCGUAGAAAAUCUGGCUGUGGAUG----UUUUUUGUUUGGCCAGCCACACGUCGUGGUUAUAAAUUAUUUUUUGCUCCUGCUCCAGCCUUUGCUGGCUUUGCUUC
.(--(-((((((((.(((((..(((((((..((..----...))..)..))))))((((.....))))..........)))))))))))))))(((((....)))))......... ( -39.30)
>DroPse_CAF1 13290 114 - 1
AUUGGGCUACAGUACAAAAAAUCUGGCUCUGGUUUGAAUUUUUUUUUCGGGCCAGCCACACGUCGUGGUUAUAAAUUAUUUUU--CCCCUGCUCGGUUCUUGCUCGGUUUUUCUUU
(((((((...((.......((((.(((.((((((((((.......))))))))))((((.....))))...............--.....))).)))))).)))))))........ ( -24.71)
>DroSec_CAF1 5589 109 - 1
UG--G-GAGGAGCGUAAAAAAUCUGGCUGUGGAUG----UUUUUUGUUUGGCCAGCCACACGUCGUGGUUAUAAAUUAUUUUUUGCUCCUGCUCCCGCCUUUGUUGGCUUUCCUUC
.(--(-(((.((.((((((((((((((((..((..----...))..)..))))))((((.....)))).........)))))))))..)).)))))(((......)))........ ( -36.40)
>DroSim_CAF1 8610 109 - 1
UG--G-GAGGAGCGUAAAAAAUCUGGCUGUGGAUG----UUUUUUGUUUGGCCAGCCACACGUCGUGGUUAUAAAUUAUUUUUUGCUCCUGCUCCCGCCUUUGUUGGCUUUCCUUA
.(--(-(((.((.((((((((((((((((..((..----...))..)..))))))((((.....)))).........)))))))))..)).)))))(((......)))........ ( -36.40)
>DroEre_CAF1 5733 110 - 1
AU--G-GAGAAGCGUAAAAAAUCUGGCCGUGGAUGG---UUUUUUGUUUGGCCAGCCACACGUCGUGGUUAUAAAUUAUUUUUUGCUCCUGCUCCUGCUCCUGGCGGCUUUCCUUC
..--(-((((.((((((((((((((((((..((..(---....)..)))))))))((((.....)))).........))))))))).((.((....))....))..)))))))... ( -31.00)
>DroYak_CAF1 8541 104 - 1
AU--G-GAGAAGCGUAAAAAAUCUGGCUGUGGAUGG---UUUUUUGUUUGGGCAGCCACACGUCGUGGUUAUAAAUUAUUUUUUGCUUCU------GCUCCUGGCUGCUCUCCUUC
..--(-((((.(((((((((((.((((((((((..(---....)..)))..)))))))(((...)))..........)))))))))....------((.....)).)))))))... ( -28.80)
>consensus
AU__G_GAGGAGCGUAAAAAAUCUGGCUGUGGAUG____UUUUUUGUUUGGCCAGCCACACGUCGUGGUUAUAAAUUAUUUUUUGCUCCUGCUCCCGCCUUUGUCGGCUUUCCUUC
.......(((((((.((((...(((((((...................)))))))((((.....))))..........)))).)))))))......(((......)))........ (-20.61 = -21.31 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:49 2006