Locus 10212

Sequence ID	3R_DroMel_CAF1
Location	27,395,359 – 27,395,470
Length	111
Max. P	0.994082

overview

Window 0

Location	27,395,359 – 27,395,470
Length	111
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	76.62
Mean single sequence MFE	-39.54
Consensus MFE	-23.66
Energy contribution	-26.54
Covariance contribution	2.88
Combinations/Pair	1.30
Mean z-score	-2.54
Structure conservation index	0.60
SVM decision value	2.45
SVM RNA-class probability	0.994082
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27395359 111 + 27905053
CAUGCUGUGUUCUUUUCCCCUUUUUCCUUUUUUUUAUGGGCUUGGCUUUGGCCUAGCCGCAUCUU---GAAGAGGGAACACGGAGGCUGGGGAAUAGAGGAUGGCUUGCUUGUU
((.(((((.((((.((((((..((((((((((...(((((((.(((....))).)))).)))...---))))))))))(.....)...)))))).)))).))))).))...... ( -43.50)
>DroSec_CAF1 11441 106 + 1
CAUGCUGUGUUCUUUUCUCCUUUUUCCUUU-UUUUAUGGGCUUGGCCU-AGCCAAGAUGCGGCU------AGAGGGAACACGGAGGGUGGAGGAGAGAGGAGGGCUUGCUUGUU
((.((.((.(((((((((((((..((((((-.....((..(((...((-((((.......))))------)).)))..)).))))))..))))))))))))).))..)).)).. ( -42.60)
>DroSim_CAF1 11488 110 + 1
CAUGCUGUGUUCUUUUCUCCUUUUUCCUUA-UUUUAUGGGCUUGGCUUUGGCCUAGCCGCAUCUU---GAAGGGGGAACACGGAGGGUGGAGGAGAGAGGAGGGCUUGCUUGUU
((.((.((.(((((((((((((.(((((..-(((.(((((((.(((....))).)))).)))...---)))..)))))(((.....)))))))))))))))).))..)).)).. ( -45.90)
>DroEre_CAF1 12112 103 + 1
CAUGCUGUGCUCUUUACC----------UU-UUUUAUGGGCUUGGUUUUGGCCCAGCCGCAUCAGGAGGAAGAGGGGAAAUGGAGGCUGAGAAGCAGAGGAUGGCUUGCCGGUU
((.(((((.((((...((----------((-((((.((((((.......)))))).((......))..)))))))).........(((....))))))).))))).))...... ( -32.90)
>DroYak_CAF1 11504 102 + 1
CAUGCUGUGUUCCUUACC--------CUUU-UUUUAUGGGCUUGGUUUUGGCCUAGCCGCAUCGU---GAAGAGGGGAUACGGAGGCCGAGAAGAAGUGGAUGGUCUGCCGGUU
................((--------((((-((..(((((((.(((....))).)))).)))...---))))))))....(((((((((............)))))).)))... ( -32.80)
>consensus
CAUGCUGUGUUCUUUUCCCCUUUUUCCUUU_UUUUAUGGGCUUGGCUUUGGCCUAGCCGCAUCUU___GAAGAGGGAACACGGAGGCUGGGGAAGAGAGGAUGGCUUGCUUGUU
((.(((((.(((((((((((..(((((.........((((((.(((....))).)))).))............(......))))))..))))))))))).))))).))...... (-23.66 = -26.54 +   2.88)

alignment

secondary structure

dotplot

Window 1

Location	27,395,359 – 27,395,470
Length	111
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	76.62
Mean single sequence MFE	-25.71
Consensus MFE	-10.68
Energy contribution	-11.92
Covariance contribution	1.24
Combinations/Pair	1.29
Mean z-score	-2.07
Structure conservation index	0.42
SVM decision value	0.79
SVM RNA-class probability	0.850565
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27395359 111 - 27905053
AACAAGCAAGCCAUCCUCUAUUCCCCAGCCUCCGUGUUCCCUCUUC---AAGAUGCGGCUAGGCCAAAGCCAAGCCCAUAAAAAAAAGGAAAAAGGGGAAAAGAACACAGCAUG
.........((.....(((.((((((.((....)).((((......---...(((.((((.(((....))).)))))))........))))...)))))).))).....))... ( -30.13)
>DroSec_CAF1 11441 106 - 1
AACAAGCAAGCCCUCCUCUCUCCUCCACCCUCCGUGUUCCCUCU------AGCCGCAUCUUGGCU-AGGCCAAGCCCAUAAAA-AAAGGAAAAAGGAGAAAAGAACACAGCAUG
............(((((.(.((((.(((.....))).....(((------(((((.....)))))-)))..............-..)))).).)))))................ ( -21.30)
>DroSim_CAF1 11488 110 - 1
AACAAGCAAGCCCUCCUCUCUCCUCCACCCUCCGUGUUCCCCCUUC---AAGAUGCGGCUAGGCCAAAGCCAAGCCCAUAAAA-UAAGGAAAAAGGAGAAAAGAACACAGCAUG
.....((......((...((((((.(((.....))).....((((.---...(((.((((.(((....))).)))))))....-.))))....))))))...)).....))... ( -26.30)
>DroEre_CAF1 12112 103 - 1
AACCGGCAAGCCAUCCUCUGCUUCUCAGCCUCCAUUUCCCCUCUUCCUCCUGAUGCGGCUGGGCCAAAACCAAGCCCAUAAAA-AA----------GGUAAAGAGCACAGCAUG
....(((((((........))))....)))..........(((((...(((.(((.((((((.......)).)))))))....-.)----------))..)))))......... ( -23.40)
>DroYak_CAF1 11504 102 - 1
AACCGGCAGACCAUCCACUUCUUCUCGGCCUCCGUAUCCCCUCUUC---ACGAUGCGGCUAGGCCAAAACCAAGCCCAUAAAA-AAAG--------GGUAAGGAACACAGCAUG
.....((...................((((((((((((........---..)))))))..)))))....((..((((......-...)--------)))..))......))... ( -27.40)
>consensus
AACAAGCAAGCCAUCCUCUCUUCCCCAGCCUCCGUGUUCCCUCUUC___AAGAUGCGGCUAGGCCAAAGCCAAGCCCAUAAAA_AAAGGAAAAAGGGGAAAAGAACACAGCAUG
.........((.....(((...((((.......(((((.............)))))((((.(((....))).))))..................))))...))).....))... (-10.68 = -11.92 +   1.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:51:31 2006