Locus 3206

Sequence ID 2L_DroMel_CAF1
Location 9,165,472 – 9,165,565
Length 93
Max. P 0.999636
window5095 window5096

overview

Window 5

Location 9,165,472 – 9,165,565
Length 93
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 67.24
Mean single sequence MFE -20.76
Consensus MFE -9.95
Energy contribution -10.91
Covariance contribution 0.96
Combinations/Pair 1.16
Mean z-score -1.87
Structure conservation index 0.48
SVM decision value 0.95
SVM RNA-class probability 0.887929
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9165472 93 + 22407834
GUAGAUCUCUUCAAAGUUUACUUCGCUUUA----------GGCAAACAUGCAAACAUUCAAGCGAAAUGCACUUUGUAC--AGA--UUU--GUUG--UUUGUUGUUUUUAA
.(((((((...((((((.((.(((((((..----------.(((....)))........))))))).)).))))))...--)))--)))--)...--.............. ( -20.20)
>DroSec_CAF1 2140 85 + 1
GUAAAUCUCCUCAAAGUUUACUUCGCUUAA----------UGCAAACAUGCAAACAUAUAAGCGAAAUGCACUUUGCUA--AGUUUUU-----------UGUUGUUU---A
...........((((((.((.((((((((.----------((((....))))......)))))))).)).))))))...--.......-----------........---. ( -15.90)
>DroSim_CAF1 2136 92 + 1
GUAAAUCUCCUCAAAGUUUACUUCGCUUUA----------UGCAAACAUGCAAACAUAUAAGCGAAAUGCACUUUGCAA--AGUUGUUU--GUUG--UUUGUUGUUU---A
(((((.((......)))))))...((....----------.))(((((.(((((((.((((((((..(((.....))).--..))))))--))))--))))))))))---. ( -23.00)
>DroEre_CAF1 2002 108 + 1
UGAAAUCCCUGCAAAGCUCAGUUCGCUUCCAUGAUUUUACGGUAUAUAUGCCAACAUAUAAGCGAAAUGCACUUUGUACAAAGUUGCACAGAUCG--UUUGUUGCU-UCCA
(((((((..((..((((.......)))).)).))))))).((((....))))..((.((((((((..((((((((....)))).))))....)))--)))))))..-.... ( -21.50)
>DroYak_CAF1 2244 101 + 1
UUAAAUCUCUUCAAAGCUUACUUCGCUUCAACGAAUUUAAUGUACAUAU--------ACAUGCGAAAUGCACUUUGCAU--AUGUGUACAGAUCGAUUUUGUUGUUGUUUA
.............((((.......))))(((((((.((..(((((((((--------(..((((((......)))))))--)))))))))....)).)))))))....... ( -23.20)
>consensus
GUAAAUCUCUUCAAAGUUUACUUCGCUUCA__________UGCAAACAUGCAAACAUAUAAGCGAAAUGCACUUUGCAA__AGUUGUUC__AUCG__UUUGUUGUUUU__A
...........((((((.((.(((((((............((((....)))).......))))))).)).))))))................................... ( -9.95 = -10.91 +   0.96)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,165,472 – 9,165,565
Length 93
Sequences 5
Columns 111
Reading direction reverse
Mean pairwise identity 67.24
Mean single sequence MFE -24.64
Consensus MFE -14.49
Energy contribution -14.90
Covariance contribution 0.41
Combinations/Pair 1.15
Mean z-score -3.23
Structure conservation index 0.59
SVM decision value 3.82
SVM RNA-class probability 0.999636
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9165472 93 - 22407834
UUAAAAACAACAAA--CAAC--AAA--UCU--GUACAAAGUGCAUUUCGCUUGAAUGUUUGCAUGUUUGCC----------UAAAGCGAAGUAAACUUUGAAGAGAUCUAC
..............--....--..(--(((--.(.((((((..(((((((((........(((....))).----------..)))))))))..)))))).).)))).... ( -21.70)
>DroSec_CAF1 2140 85 - 1
U---AAACAACA-----------AAAAACU--UAGCAAAGUGCAUUUCGCUUAUAUGUUUGCAUGUUUGCA----------UUAAGCGAAGUAAACUUUGAGGAGAUUUAC
.---........-----------.....((--(..((((((..((((((((((......((((....))))----------.))))))))))..))))))..)))...... ( -25.60)
>DroSim_CAF1 2136 92 - 1
U---AAACAACAAA--CAAC--AAACAACU--UUGCAAAGUGCAUUUCGCUUAUAUGUUUGCAUGUUUGCA----------UAAAGCGAAGUAAACUUUGAGGAGAUUUAC
.---..........--....--......((--(..((((((..(((((((((.(((((..(....)..)))----------)))))))))))..))))))..)))...... ( -24.80)
>DroEre_CAF1 2002 108 - 1
UGGA-AGCAACAAA--CGAUCUGUGCAACUUUGUACAAAGUGCAUUUCGCUUAUAUGUUGGCAUAUAUACCGUAAAAUCAUGGAAGCGAACUGAGCUUUGCAGGGAUUUCA
.(((-((((.((..--.....)))))..(((((..((((((.((.((((((((((((....)))))...((((......))))))))))).)).))))))))))).)))). ( -29.10)
>DroYak_CAF1 2244 101 - 1
UAAACAACAACAAAAUCGAUCUGUACACAU--AUGCAAAGUGCAUUUCGCAUGU--------AUAUGUACAUUAAAUUCGUUGAAGCGAAGUAAGCUUUGAAGAGAUUUAA
............(((((....((((((..(--(((((...(((.....))))))--------)))))))))......((.(..((((.......))))..).))))))).. ( -22.00)
>consensus
U__AAAACAACAAA__CAAC__AAACAACU__GUGCAAAGUGCAUUUCGCUUAUAUGUUUGCAUGUUUGCA__________UAAAGCGAAGUAAACUUUGAAGAGAUUUAC
...................................((((((..((((((((((((((....))))).................)))))))))..))))))........... (-14.49 = -14.90 +   0.41)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:57 2006