Locus 2127

Sequence ID	3R_DroMel_CAF1
Location	6,091,041 – 6,091,162
Length	121
Max. P	0.974673

overview

Window 4

Location	6,091,041 – 6,091,133
Length	92
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	79.93
Mean single sequence MFE	-29.63
Consensus MFE	-15.31
Energy contribution	-16.15
Covariance contribution	0.84
Combinations/Pair	1.16
Mean z-score	-2.21
Structure conservation index	0.52
SVM decision value	0.33
SVM RNA-class probability	0.692039
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6091041 92 + 27905053
AGCGAUGAACUCCCUCGCGCUCUGAUCAGAACGGG---AAGAAGAAGCAGCCGCAUUUGCAGCUGCGCCGAGCGAUCAUUUUCGCAUACUUCUUU
.((((.(.....).))))(.(((....))).)..(---((((((..(((((.((....)).))))).....((((......))))...))))))) ( -30.40)
>DroSec_CAF1 3034 92 + 1
AGCGAUGAACUCCCUCGCGUUCUGAUCAGAACAGG---AAGAAGAAGCAGUCGCAUUUGCAGCUGCGCCGAGCGAUCAUUUUCGCAUACUUCUUU
.((((.(.....).))))(((((....)))))..(---((((((..(((((.((....)).))))).....((((......))))...))))))) ( -33.00)
>DroSim_CAF1 3018 92 + 1
AGCGAUGAACUCCCUCGCGUUCUGAUCAGAACAGG---AAGAAGAAGCAGUCGCAUUUGCAGCUGCGCCCAGCGAUCAUUUUCGCAUACUUCUUU
.((((.(.....).))))(((((....)))))..(---((((((..(((((.((....)).))))).....((((......))))...))))))) ( -33.00)
>DroEre_CAF1 2969 89 + 1
AGCGAUGAACUCCCUCGC--UCUGAUCAGAACGGG---AAGAAGAAGCAGCGGCAUUUGCAGCUGCGCCAAGCGAUCAUUUUCGCAUACUU-UUU
.............((((.--(((....))).))))---((((((..(((((.((....)).))))).....((((......))))...)))-))) ( -27.00)
>DroYak_CAF1 3063 92 + 1
AGCGAUGAACUCCCUCGC--UCUGAUCAGAACGGGAGGAAGAAGAAGAAGCAGCAUUUGCAGCUGCGGCAAGCGAUCAUUUUCGCAUACUU-UUU
..........(((((((.--(((....))).)))).)))..((((((..(((((.......))))).....((((......))))...)))-))) ( -27.60)
>DroPer_CAF1 3005 79 + 1
CACGAUGAACUCCCGCACUGCUUGCUCAGGCAGGG---CAGCAACAGCAAUAGCAGCUGCAGCUGCGCUUCUCCGUCAAC----CA---------
...((((.......((.((((((....)))))).(---((((..((((.......))))..))))))).....))))...----..--------- ( -26.80)
>consensus
AGCGAUGAACUCCCUCGCG_UCUGAUCAGAACGGG___AAGAAGAAGCAGCCGCAUUUGCAGCUGCGCCAAGCGAUCAUUUUCGCAUACUU_UUU
.((((.(.....).))))..(((....)))................(((((.((....)).))))).....((((......)))).......... (-15.31 = -16.15 +   0.84)

alignment

secondary structure

dotplot

Window 5

Location	6,091,041 – 6,091,133
Length	92
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	79.93
Mean single sequence MFE	-32.28
Consensus MFE	-17.84
Energy contribution	-18.35
Covariance contribution	0.51
Combinations/Pair	1.45
Mean z-score	-2.38
Structure conservation index	0.55
SVM decision value	0.79
SVM RNA-class probability	0.851918
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6091041 92 - 27905053
AAAGAAGUAUGCGAAAAUGAUCGCUCGGCGCAGCUGCAAAUGCGGCUGCUUCUUCUU---CCCGUUCUGAUCAGAGCGCGAGGGAGUUCAUCGCU
...(((((..((((......))))...))((((((((....))))))))..((((((---(.((((((....)))))).))))))))))...... ( -38.40)
>DroSec_CAF1 3034 92 - 1
AAAGAAGUAUGCGAAAAUGAUCGCUCGGCGCAGCUGCAAAUGCGACUGCUUCUUCUU---CCUGUUCUGAUCAGAACGCGAGGGAGUUCAUCGCU
...(((((..((((......))))...))((((.(((....))).))))..((((((---(.((((((....)))))).))))))))))...... ( -30.20)
>DroSim_CAF1 3018 92 - 1
AAAGAAGUAUGCGAAAAUGAUCGCUGGGCGCAGCUGCAAAUGCGACUGCUUCUUCUU---CCUGUUCUGAUCAGAACGCGAGGGAGUUCAUCGCU
..........((((......))))..(((((((.(((....))).))))..((((((---(.((((((....)))))).)))))))......))) ( -30.30)
>DroEre_CAF1 2969 89 - 1
AAA-AAGUAUGCGAAAAUGAUCGCUUGGCGCAGCUGCAAAUGCCGCUGCUUCUUCUU---CCCGUUCUGAUCAGA--GCGAGGGAGUUCAUCGCU
...-......((((......))))..((((((((.((....)).))))).....(((---((((((((....)))--))).)))))......))) ( -32.60)
>DroYak_CAF1 3063 92 - 1
AAA-AAGUAUGCGAAAAUGAUCGCUUGCCGCAGCUGCAAAUGCUGCUUCUUCUUCUUCCUCCCGUUCUGAUCAGA--GCGAGGGAGUUCAUCGCU
...-..(((.((((......)))).))).(((((.......)))))........(((((((..(((((....)))--)))))))))......... ( -28.90)
>DroPer_CAF1 3005 79 - 1
---------UG----GUUGACGGAGAAGCGCAGCUGCAGCUGCUAUUGCUGUUGCUG---CCCUGCCUGAGCAAGCAGUGCGGGAGUUCAUCGUG
---------..----....(((..(((..(((((.(((((.......))))).))))---)((((((((......))).)))))..)))..))). ( -33.30)
>consensus
AAA_AAGUAUGCGAAAAUGAUCGCUCGGCGCAGCUGCAAAUGCGACUGCUUCUUCUU___CCCGUUCUGAUCAGA_CGCGAGGGAGUUCAUCGCU
..........((((......((.((((..((((..((....))..)))).............((((((....)))))))))).)).....)))). (-17.84 = -18.35 +   0.51)

alignment

secondary structure

dotplot

Window 6

Location	6,091,060 – 6,091,162
Length	102
Sequences	5
Columns	105
Reading direction	forward
Mean pairwise identity	93.30
Mean single sequence MFE	-28.20
Consensus MFE	-23.82
Energy contribution	-23.74
Covariance contribution	-0.08
Combinations/Pair	1.08
Mean z-score	-1.92
Structure conservation index	0.84
SVM decision value	1.73
SVM RNA-class probability	0.974673
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6091060 102 + 27905053
CUCUGAUCAGAACGGG---AAGAAGAAGCAGCCGCAUUUGCAGCUGCGCCGAGCGAUCAUUUUCGCAUACUUCUUUCUUAAUUUGUUUUUGCCGAGCCAUUUUUA
(((.(...((((((((---((((((..(((((.((....)).))))).....((((......))))...)))))))))......)))))..).)))......... ( -30.90)
>DroSec_CAF1 3053 102 + 1
UUCUGAUCAGAACAGG---AAGAAGAAGCAGUCGCAUUUGCAGCUGCGCCGAGCGAUCAUUUUCGCAUACUUCUUUCUUAAUUUGUUUUUGCCGAGCCAUUUUUA
.......((((..(((---((((((..(((((.((....)).))))).....((((......))))...)))))))))...)))).................... ( -27.60)
>DroSim_CAF1 3037 102 + 1
UUCUGAUCAGAACAGG---AAGAAGAAGCAGUCGCAUUUGCAGCUGCGCCCAGCGAUCAUUUUCGCAUACUUCUUUCUUAAUUUGUUUUUGCCGAGCCAUUUUUA
.......((((..(((---((((((..(((((.((....)).))))).....((((......))))...)))))))))...)))).................... ( -27.60)
>DroEre_CAF1 2987 100 + 1
-UCUGAUCAGAACGGG---AAGAAGAAGCAGCGGCAUUUGCAGCUGCGCCAAGCGAUCAUUUUCGCAUACUU-UUUCUUAAUUUGUUUGUGCCGAGCCAUUUUUA
-......((((..(((---((((((..(((((.((....)).))))).....((((......))))...)))-))))))..)))).................... ( -27.60)
>DroYak_CAF1 3081 103 + 1
-UCUGAUCAGAACGGGAGGAAGAAGAAGAAGCAGCAUUUGCAGCUGCGGCAAGCGAUCAUUUUCGCAUACUU-UUUCUUAAUUUGUUUUUGCCAAGCCAUUUUUA
-.((...(((((..(((..(((((((((..(((((.......))))).....((((......))))...)))-))))))..)))..)))))...))......... ( -27.30)
>consensus
_UCUGAUCAGAACGGG___AAGAAGAAGCAGCCGCAUUUGCAGCUGCGCCAAGCGAUCAUUUUCGCAUACUUCUUUCUUAAUUUGUUUUUGCCGAGCCAUUUUUA
........((((((((...((((((..(((((.((....)).))))).....((((......)))).......))))))..))))))))................ (-23.82 = -23.74 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:28:07 2006