Locus 1619

Sequence ID	3R_DroMel_CAF1
Location	4,688,611 – 4,688,748
Length	137
Max. P	0.998034

overview

Window 6

Location	4,688,611 – 4,688,731
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	87.01
Mean single sequence MFE	-36.70
Consensus MFE	-29.45
Energy contribution	-30.15
Covariance contribution	0.70
Combinations/Pair	1.10
Mean z-score	-1.78
Structure conservation index	0.80
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4688611 120 - 27905053
GUUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCGCUUGUUCCAAGCACGCUUAAACUCGAAAACAUUUGAUACGUG
.(((((((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))(((((...)))))............)))).............. ( -35.50)
>DroPse_CAF1 47139 113 - 1
UGUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCGCUUGUGUAUUGUCGUUUUAAACGGGAAUAA-----GUACG--
....((((((((.((((.......))))......((((((.....)))))).((((........))))..))))))))...(((((((.((((.....)))).)))).-----.))).-- ( -35.10)
>DroSec_CAF1 37997 120 - 1
GUGUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCGCUUGUUUCAAGCACGCUUAAACUCGAAAACAUUUGAUACGUG
((((((((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))(((((...)))))......................)))))... ( -39.20)
>DroSim_CAF1 40528 120 - 1
GUGUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCGCUUGUUUCAAGCACGCUUAAACUCGAAAACAUUUGAUACGUG
((((((((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))(((((...)))))......................)))))... ( -39.20)
>DroAna_CAF1 39003 120 - 1
AUUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCACUUGAUGUAACCUGGCUUAAGCUGGAAAACAUUUGAUACGUG
.....(((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))....(((((...(..((....))..)...)))))......... ( -36.10)
>DroPer_CAF1 48048 113 - 1
UAUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCGCUUGUGUAUUGUCGUUUUAAACGGGAAUAA-----GUACG--
....((((((((.((((.......))))......((((((.....)))))).((((........))))..))))))))...(((((((.((((.....)))).)))).-----.))).-- ( -35.10)
>consensus
GUUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCGCUUGUUUCAAGCACGCUUAAACUCGAAAACAUUUGAUACGUG
.(((((((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))((((.....))))............)))).............. (-29.45 = -30.15 +   0.70)

alignment

secondary structure

dotplot

Window 7

Location	4,688,651 – 4,688,748
Length	97
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	85.88
Mean single sequence MFE	-35.06
Consensus MFE	-33.00
Energy contribution	-33.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.17
Structure conservation index	0.94
SVM decision value	1.90
SVM RNA-class probability	0.981853
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4688651 97 + 27905053
AGCGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAAACCAAAGUAU--U--------------AUUUUUUU
..((((((((..((((........)))).((((((....).))))).....(((((.......)))))))))))))............--.--------------........ ( -33.40)
>DroPse_CAF1 47172 112 + 1
AGCGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAACACAAAGUAUCUUUUUUUCGCUUUUUUUUCUU-UU
((((((((((..((((........)))).((((((....).))))).....(((((.......))))))))))))(((...((((...))))..))))))..........-.. ( -34.00)
>DroEre_CAF1 41127 109 + 1
AGCGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGACACUAAAGUAAUUUUUUUUUUU--UUUUUAC-U-UU
.(((((((((..((((........)))).((((((....).))))).....(((((.......))))))))))))).)...(((((((...........--...))))-)-)) ( -35.84)
>DroPer_CAF1 48081 112 + 1
AGCGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAAUAGAAAGUAUCCUUUUUUCGCUUUUUUUUCUU-UU
...(((((((..((((........)))).((((((....).))))).....(((((.......))))))))))))(((.(((((((...........))))))).)))..-.. ( -37.00)
>consensus
AGCGACCGUGUGGCCUAAUGGAUAAGGCGUCGGACUUCGGAUCCGAAGAUUGCAGGUUCGAGUCCUGUCACGGUCGAAAACAAAGUAUCUUUUUUUCGC__UUUUUUCUU_UU
..((((((((..((((........))))...(((((.((((((.(.......).)))))))))))...))))))))..................................... (-33.00 = -33.00 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	4,688,651 – 4,688,748
Length	97
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	85.88
Mean single sequence MFE	-31.93
Consensus MFE	-29.50
Energy contribution	-29.50
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-3.06
Structure conservation index	0.92
SVM decision value	2.99
SVM RNA-class probability	0.998034
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4688651 97 - 27905053
AAAAAAAU--------------A--AUACUUUGGUUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCGCU
........--------------.--............((((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))).. ( -29.50)
>DroPse_CAF1 47172 112 - 1
AA-AAGAAAAAAAAGCGAAAAAAAGAUACUUUGUGUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCGCU
..-..........((((((..((((...))))...)))(((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))))) ( -33.30)
>DroEre_CAF1 41127 109 - 1
AA-A-GUAAAAA--AAAAAAAAAAAUUACUUUAGUGUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCGCU
((-(-((((...--...........)))))))...(.((((((((.((((.......))))......((((((.....)))))).((((........))))..))))))))). ( -31.74)
>DroPer_CAF1 48081 112 - 1
AA-AAGAAAAAAAAGCGAAAAAAGGAUACUUUCUAUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCGCU
..-..........((((((.((((....))))...)))(((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))))) ( -33.20)
>consensus
AA_AAGAAAAAA__GCGAAAAAAAGAUACUUUGGUUUCGACCGUGACAGGACUCGAACCUGCAAUCUUCGGAUCCGAAGUCCGACGCCUUAUCCAUUAGGCCACACGGUCGCU
.....................................((((((((.((((.......))))......((((((.....)))))).((((........))))..)))))))).. (-29.50 = -29.50 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:01 2006