Locus 1988

Sequence ID	3L_DroMel_CAF1
Location	5,465,457 – 5,465,654
Length	197
Max. P	0.930433

overview

Window 3

Location	5,465,457 – 5,465,575
Length	118
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	94.68
Mean single sequence MFE	-27.72
Consensus MFE	-24.64
Energy contribution	-24.36
Covariance contribution	-0.28
Combinations/Pair	1.08
Mean z-score	-1.53
Structure conservation index	0.89
SVM decision value	1.21
SVM RNA-class probability	0.930433
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5465457 118 + 23771897
UAAGGGAAACUGCUGAGAACAUCGUUUGAAGGCAAUAACAACAUUUGCCAUGCUCCAUUGUUUUUUUGCUACUUAAAUUGCAGUUCUCUGCUGGUGUUUUCGUUCUCCAACU-UUUGUU
...((..(((....(((((((((((((((.(((((.(((((.....((...))....)))))...)))))..)))))).((((....)))).))))))))))))..))....-...... ( -28.40)
>DroSec_CAF1 26985 118 + 1
UAAGGGAAACUGCUGAGAACAUCGUUUGAAGGCAAUAACAACAUUUGCCAUGCUCCAUUGUUUUUUU-CUACUUAAAUUGCAGUUCUCUGCUGGUGUUUUCGUUCUCCAAGGGCAUAAC
....((((((.((.((((((..........(((((.........))))).(((......((......-..)).......))))))))).))....))))))((((.....))))..... ( -27.42)
>DroSim_CAF1 28433 118 + 1
UAAGGGAAACUGCUGAGAACAUCGUUUGAAGGCAAUAACAACAUUUGCCAUGCUCCAUUGUUUUUUUGCUACUUAAAUUGCAGUUCUCUGCUGGUGUUUUCGUUCUCCAACU-UUUGUU
...((..(((....(((((((((((((((.(((((.(((((.....((...))....)))))...)))))..)))))).((((....)))).))))))))))))..))....-...... ( -28.40)
>DroEre_CAF1 26630 118 + 1
UAAGGGAAACUGCUGAGAACAUCGUUUGAAGGCAAUAACAACAUUUGCCAUGCUCCAUUGUUUUUUUGCUACUUAAAUUGCUGUUCUCUGUUGGUGUUUCCGUUCUCCAACU-UUCGUU
....((((((.((.(((((((.(((((((.(((((.(((((.....((...))....)))))...)))))..))))).)).))))))).))....))))))...........-...... ( -28.00)
>DroYak_CAF1 14441 118 + 1
UACGGGAAACUGCUGAGAACAUCGUUUGAAGGCAAUAACAACAUUUGCCAUGCUCCAUUGUUUUUUUGCUACUUAAAUUGCAGUUCUCUGUUGGUGUUUCCGUUCUCCAACU-UUUGCU
..(((....)))..((((((...((((((.(((((.(((((.....((...))....)))))...)))))..))))))....)))))).(((((.(........).))))).-...... ( -26.40)
>consensus
UAAGGGAAACUGCUGAGAACAUCGUUUGAAGGCAAUAACAACAUUUGCCAUGCUCCAUUGUUUUUUUGCUACUUAAAUUGCAGUUCUCUGCUGGUGUUUUCGUUCUCCAACU_UUUGUU
....((((((.((.((((((..........(((((.........))))).........(((..(((........)))..))))))))).))....)))))).................. (-24.64 = -24.36 +  -0.28)

alignment

secondary structure

dotplot

Window 4

Location	5,465,536 – 5,465,654
Length	118
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	78.30
Mean single sequence MFE	-28.02
Consensus MFE	-16.53
Energy contribution	-17.21
Covariance contribution	0.69
Combinations/Pair	1.31
Mean z-score	-1.90
Structure conservation index	0.59
SVM decision value	0.29
SVM RNA-class probability	0.669400
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5465536 118 + 23771897
GCAGUUCUCUGCUGGUGUUUUCGUUCUCCAACU-UUUGUUAUACCCUUGUAAAGGGUAUUAUGAUUUUGAUAAGAACUUUGUAGUGCAGAAAUAGCUCAAUGCA-UACAUACAUAUAAAU
((((....))))..((((....(((((.(((..-.(..(.(((((((.....))))))).)..)..)))...)))))..((((.((((............))))-)))).))))...... ( -25.80)
>DroSec_CAF1 27063 114 + 1
GCAGUUCUCUGCUGGUGUUUUCGUUCUCCAAGGGCAUAACAAAACCUUGUAAAGGGUAUUAUGAUUUUGACAAGAACUGUGUAGUG---AAAUAGCUUAUUACUGUUCA---AAACACAU
((((....))))..(((((((.......(((((.(((((....(((((....))))).))))).)))))....((((...((((((---(......))))))).)))))---)))))).. ( -29.00)
>DroSim_CAF1 28512 113 + 1
GCAGUUCUCUGCUGGUGUUUUCGUUCUCCAACU-UUUGUUAUACCCUUGUAAAGGGUAUUAUGAUUUUGAUAAGAACUAUGUAGUG---AAAUAGCUUAUUACUGUUCA---AAACACAU
((((....))))..(((((((.......(((..-.(..(.(((((((.....))))))).)..)..)))....((((...((((((---(......))))))).)))))---)))))).. ( -30.00)
>DroYak_CAF1 14520 116 + 1
GCAGUUCUCUGUUGGUGUUUCCGUUCUCCAACU-UUUGCUAUAUCCUUGCCAAGGGUAUAACAAUUUUGAUAAGAAUUUGGAGGAGCAGAAGUGGCACUAAACUAUAAA---AAAUACUU
((((....))))(((((((((.(((((((((..-.(((.((((((((.....)))))))).)))((((....)))).))))).)))).)))...)))))).........---........ ( -27.30)
>consensus
GCAGUUCUCUGCUGGUGUUUUCGUUCUCCAACU_UUUGUUAUACCCUUGUAAAGGGUAUUAUGAUUUUGAUAAGAACUUUGUAGUG___AAAUAGCUCAAUACUGUACA___AAACACAU
((((....))))..((((((..(((((........((((.(((((((.....))))))).))))........)))))...((((((...........)))))).........)))))).. (-16.53 = -17.21 +   0.69)

alignment

secondary structure

dotplot

Window 5

Location	5,465,536 – 5,465,654
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	78.30
Mean single sequence MFE	-25.25
Consensus MFE	-14.64
Energy contribution	-15.70
Covariance contribution	1.06
Combinations/Pair	1.05
Mean z-score	-2.16
Structure conservation index	0.58
SVM decision value	0.83
SVM RNA-class probability	0.862364
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5465536 118 - 23771897
AUUUAUAUGUAUGUA-UGCAUUGAGCUAUUUCUGCACUACAAAGUUCUUAUCAAAAUCAUAAUACCCUUUACAAGGGUAUAACAAA-AGUUGGAGAACGAAAACACCAGCAGAGAACUGC
...........((((-((((..((....))..)))).)))).(((((((............(((((((.....)))))))......-.(((((.(........).))))).))))))).. ( -27.70)
>DroSec_CAF1 27063 114 - 1
AUGUGUUU---UGAACAGUAAUAAGCUAUUU---CACUACACAGUUCUUGUCAAAAUCAUAAUACCCUUUACAAGGUUUUGUUAUGCCCUUGGAGAACGAAAACACCAGCAGAGAACUGC
.(((((..---((((.(((.....)))..))---))..)))))((((((..(((...(((((((.(((.....)))...)))))))...)))))))))..........((((....)))) ( -24.40)
>DroSim_CAF1 28512 113 - 1
AUGUGUUU---UGAACAGUAAUAAGCUAUUU---CACUACAUAGUUCUUAUCAAAAUCAUAAUACCCUUUACAAGGGUAUAACAAA-AGUUGGAGAACGAAAACACCAGCAGAGAACUGC
.(((((..---((((.(((.....)))..))---))..)))))((((((............(((((((.....)))))))......-.(((((.(........).))))).))))))... ( -27.10)
>DroYak_CAF1 14520 116 - 1
AAGUAUUU---UUUAUAGUUUAGUGCCACUUCUGCUCCUCCAAAUUCUUAUCAAAAUUGUUAUACCCUUGGCAAGGAUAUAGCAAA-AGUUGGAGAACGGAAACACCAACAGAGAACUGC
........---....((((((((.....))((((...((((((...(((.......((((((((.(((.....))).)))))))))-))))))))...(....).....)))))))))). ( -21.81)
>consensus
AUGUAUUU___UGAACAGUAAUAAGCUAUUU___CACUACAAAGUUCUUAUCAAAAUCAUAAUACCCUUUACAAGGGUAUAACAAA_AGUUGGAGAACGAAAACACCAGCAGAGAACUGC
..........................................(((((((............(((((((.....)))))))........(((((.(........).))))).))))))).. (-14.64 = -15.70 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:54 2006