Locus 6368

Sequence ID	3R_DroMel_CAF1
Location	16,701,507 – 16,701,605
Length	98
Max. P	0.987518

overview

Window 0

Location	16,701,507 – 16,701,605
Length	98
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	77.14
Mean single sequence MFE	-36.02
Consensus MFE	-16.61
Energy contribution	-19.75
Covariance contribution	3.14
Combinations/Pair	1.21
Mean z-score	-3.02
Structure conservation index	0.46
SVM decision value	2.08
SVM RNA-class probability	0.987518
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16701507 98 + 27905053
-UUCAGCCAUGGGCAACAAAAAGCCAUCCUGCUGCGUAGGGUGUCCUUUUCUCUG--------CCUGCGCCCUUUGCUAAGACG-UGCUUACAAGGGUUCACGGCUGU
-..(((((..(((((...(((((.((((((((...))))))))..)))))...))--------)))(.((((((.(.((((...-..))))))))))).)..))))). ( -37.40)
>DroSec_CAF1 24213 98 + 1
-UUCAGCCAUGGGCAGCAAAAAGCCAUCCUGCUGCGUAGGGUGUCCUUUUUUCUG--------CCUGCGCCCUUUGCUAAGACG-UGCUUACAAGGGUUCUCGGCUGU
-..(((((..((((((.((((((.((((((((...))))))))..)))))).)))--------)))(.((((((.(.((((...-..))))))))))).)..))))). ( -42.20)
>DroSim_CAF1 24157 98 + 1
-UUCAGCCAUGGGCAGCAAAAAGCCAUCCUGCUGCGUAGGAUGUCCUUUUUUCUG--------CCUGCGCCCUUUGCUAAGACG-UGCUUACAAGGGUUCUCGGCUGU
-..(((((..((((((.((((((.((((((((...))))))))..)))))).)))--------)))(.((((((.(.((((...-..))))))))))).)..))))). ( -42.80)
>DroEre_CAF1 21945 96 + 1
-UUCAGCCUUAGAGCGCAAAAAGCCGUCCUGCUGCAUAGGGUGUCCUUUUUUCUG--------CCUG--CCCUUUGCUAAGAUG-UGCUUACAAGGGUUCUCGGCUGU
-..(((((..(((((.(...((((((((.....(((.((((((..(........)--------..))--)))).)))...))))-.))))....).))))).))))). ( -32.70)
>DroYak_CAF1 27874 96 + 1
-UUCAGCCUUGGGGCUCAAAAAGCCGUACAGCUGCAUAGGGUGUUCUUAUUUCUG--------CCUG--CCCUUUGCUAAGACG-UGCUUACAAGGGUUCCUGGCUGU
-..(((((..(((((((...(((((((......(((.((((((..(........)--------..))--)))).)))....)))-.))))....))))))).))))). ( -36.20)
>DroAna_CAF1 15991 96 + 1
AAUUAUCCUAGUGCAGAAUAAAGUC----UG-UGACUGGAGUAAGCUUUUCUUUGGGCCAUGUCACACACCGUUUGCUAAGCCGUUGCUUACAAGGACUC-------U
.....((((.(((((((.....((.----((-(((((((..((((......))))..))).)))))).))..))))).((((....)))))).))))...-------. ( -24.80)
>consensus
_UUCAGCCAUGGGCAGCAAAAAGCCAUCCUGCUGCGUAGGGUGUCCUUUUUUCUG________CCUGCGCCCUUUGCUAAGACG_UGCUUACAAGGGUUCUCGGCUGU
...(((((..((((((.((((((.(((((((.....)))))))..)))))).)))........)))....((((((.((((......)))))))))).....))))). (-16.61 = -19.75 +   3.14)

alignment

secondary structure

dotplot

Window 1

Location	16,701,507 – 16,701,605
Length	98
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	77.14
Mean single sequence MFE	-31.20
Consensus MFE	-14.68
Energy contribution	-17.52
Covariance contribution	2.84
Combinations/Pair	1.13
Mean z-score	-2.04
Structure conservation index	0.47
SVM decision value	0.28
SVM RNA-class probability	0.668054
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16701507 98 - 27905053
ACAGCCGUGAACCCUUGUAAGCA-CGUCUUAGCAAAGGGCGCAGG--------CAGAGAAAAGGACACCCUACGCAGCAGGAUGGCUUUUUGUUGCCCAUGGCUGAA-
.((((((((..(((((....((.-.......)).)))))....((--------(((.((((((..((.(((.......))).)).)))))).)))))))))))))..- ( -35.90)
>DroSec_CAF1 24213 98 - 1
ACAGCCGAGAACCCUUGUAAGCA-CGUCUUAGCAAAGGGCGCAGG--------CAGAAAAAAGGACACCCUACGCAGCAGGAUGGCUUUUUGCUGCCCAUGGCUGAA-
.((((((.(..(((((....((.-.......)).)))))..).((--------(((.((((((..((.(((.......))).)).)))))).)))))..))))))..- ( -34.40)
>DroSim_CAF1 24157 98 - 1
ACAGCCGAGAACCCUUGUAAGCA-CGUCUUAGCAAAGGGCGCAGG--------CAGAAAAAAGGACAUCCUACGCAGCAGGAUGGCUUUUUGCUGCCCAUGGCUGAA-
.((((((.(..(((((....((.-.......)).)))))..).((--------(((.((((((..((((((.......)))))).)))))).)))))..))))))..- ( -39.00)
>DroEre_CAF1 21945 96 - 1
ACAGCCGAGAACCCUUGUAAGCA-CAUCUUAGCAAAGGG--CAGG--------CAGAAAAAAGGACACCCUAUGCAGCAGGACGGCUUUUUGCGCUCUAAGGCUGAA-
.((((((((..(((((....((.-.......)).)))))--...(--------((((((..(((....))).....((......))))))))).)))...)))))..- ( -26.70)
>DroYak_CAF1 27874 96 - 1
ACAGCCAGGAACCCUUGUAAGCA-CGUCUUAGCAAAGGG--CAGG--------CAGAAAUAAGAACACCCUAUGCAGCUGUACGGCUUUUUGAGCCCCAAGGCUGAA-
.(((((.((.......((((((.-.(((((.....))))--)..(--------((.................))).))).)))(((((...)))))))..)))))..- ( -25.13)
>DroAna_CAF1 15991 96 - 1
A-------GAGUCCUUGUAAGCAACGGCUUAGCAAACGGUGUGUGACAUGGCCCAAAGAAAAGCUUACUCCAGUCA-CA----GACUUUAUUCUGCACUAGGAUAAUU
.-------..(((((.((((((....)))).(((...(((.((((((.(((....(((.....)))...)))))))-))----.)))......))))).))))).... ( -26.10)
>consensus
ACAGCCGAGAACCCUUGUAAGCA_CGUCUUAGCAAAGGGCGCAGG________CAGAAAAAAGGACACCCUACGCAGCAGGAUGGCUUUUUGCUGCCCAAGGCUGAA_
.(((((.....(((((.((((......))))...)))))..................................(((((((((.....)))))))))....)))))... (-14.68 = -17.52 +   2.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:19:45 2006