Locus 1711

Sequence ID	2R_DroMel_CAF1
Location	6,460,557 – 6,460,686
Length	129
Max. P	0.897363

overview

Window 1

Location	6,460,557 – 6,460,657
Length	100
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	79.97
Mean single sequence MFE	-27.92
Consensus MFE	-16.89
Energy contribution	-16.42
Covariance contribution	-0.47
Combinations/Pair	1.21
Mean z-score	-2.35
Structure conservation index	0.60
SVM decision value	1.00
SVM RNA-class probability	0.897363
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6460557 100 + 20766785
-----UUUU-----UUAU-UUCUGUUGAGGCA-AAAUUGUUUGUAUUUGUUUAGGCUUAUGGCCAAGACGAUAAAAACGUCUCAAGCGCAGACAAACGCCCAGAGAAAACAA
-----....-----...(-((((.(((.(((.-...(((((((..((((....(((.....))).(((((.......)))))))))..)))))))..))))))))))).... ( -28.80)
>DroVir_CAF1 26106 105 + 1
-----UUUUUUAAGUUUU-UUGUAUCGAGAUA-AAAUUGUUUGUAUUUGUUUAGGCUUAUGGCCAAGACGAUAAAACCGUCUCAAGCGUAGACAAAUGCCAAGAGUAAACCA
-----........(((((-((((......)))-))(((.((.(((((((((((.((((.......(((((.......))))).)))).))))))))))).)).))))))).. ( -22.10)
>DroPse_CAF1 37471 102 + 1
-----UUUU-----UUCUCCAUUGUUGGGACAGAAAUUGUUUGUAUUUGUUUAGGCUUAUGGCCAAGACGAUAAAAACGUCUCGAGCGCCGACAAAUGGCCGGAGAAAGCAG
-----..((-----((((((....((((((((....).((((....((((((.(((.....))).))))))...)))))))))))(.((((.....)))))))))))))... ( -32.10)
>DroGri_CAF1 17747 105 + 1
-----UUUUGAUGAUUUU-UUUCAUCGAAAGA-AAAUGGUUUGUAUUUGCUUAGGCUUAUGGCCAAGAAGAUAAAACCGUCUCAAGCACAGACAAAUGCCAACAAUAAACCA
-----(((((((((....-..)))))))))..-...((((((((...(((((.(((.....)))..((.(((......))))))))))...))))..))))........... ( -26.60)
>DroAna_CAF1 37629 99 + 1
-----C-UG-----AGUU-UUUUGUUGAGACA-AAAUUGUUUGUAUUUGUUUAGGCUUAUGGCCAAGACGAUAAAAACGUCUCAAGCGCAGACAAAUGCCCAGAGAAAACAA
-----.-..-----.(((-((((.(((((((.-.....((((....((((((.(((.....))).))))))...)))))))))))(.(((......))).)..))))))).. ( -25.80)
>DroPer_CAF1 37140 107 + 1
UCGUUUUUU-----UGCUCCAUUGUUGGGACAGAAAUUGUUUGUAUUUGUUUAGGCUUAUGGCCAAGACGAUAAAAACGUCUCGAGCGCCGACAAAUGGCCGGAGAAAGCAG
..(((((((-----(...(((((((((((...((...(((((....((((((.(((.....))).))))))...)))))..))...).))))).)))))...)))))))).. ( -32.10)
>consensus
_____UUUU_____UUUU_UUUUGUUGAGACA_AAAUUGUUUGUAUUUGUUUAGGCUUAUGGCCAAGACGAUAAAAACGUCUCAAGCGCAGACAAAUGCCCAGAGAAAACAA
......................................((((((...(((((.(((.....))).(((((.......))))).)))))...))))))............... (-16.89 = -16.42 +  -0.47)

alignment

secondary structure

dotplot

Window 2

Location	6,460,581 – 6,460,686
Length	105
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	78.43
Mean single sequence MFE	-27.03
Consensus MFE	-18.24
Energy contribution	-18.22
Covariance contribution	-0.03
Combinations/Pair	1.11
Mean z-score	-1.46
Structure conservation index	0.67
SVM decision value	0.51
SVM RNA-class probability	0.764507
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6460581 105 + 20766785
UUGUUUGUAUUUGUUUAGGCUUAUGGCCAAGACGAUAAAAACGUCUCAAGCGCAGACAAACGCCCAGAGAAAACAA-GUG--AAUGACG-CUGACU-UGGCGCAAU-CGAA
(((((((..((((....(((.....))).(((((.......)))))))))..))))))).((((..(((......(-(((--.....))-))..))-)))))....-.... ( -27.20)
>DroVir_CAF1 26135 104 + 1
UUGUUUGUAUUUGUUUAGGCUUAUGGCCAAGACGAUAAAACCGUCUCAAGCGUAGACAAAUGCCAAGAGUAAACCAAGAA--AAUU----UGUAAA-UAUAAUAUAAUGAA
((.((.(((((((((((.((((.......(((((.......))))).)))).))))))))))).)).))...........--....----......-.............. ( -20.20)
>DroPse_CAF1 37497 107 + 1
UUGUUUGUAUUUGUUUAGGCUUAUGGCCAAGACGAUAAAAACGUCUCGAGCGCCGACAAAUGGCCGGAGAAAGCAG-GCG--GAUGACGGCCGACUUUAGAGCCAU-CGAA
..((((....((((((.(((.....))).))))))...))))...(((((.((((.....)))))((..((((..(-((.--(....).)))..))))....)).)-))). ( -31.00)
>DroMoj_CAF1 32079 106 + 1
UUGUUUGUAUUUGUUUAGGCUUAUGGCCAAGACGAUAAAACCGUCUCAAGCGCAGACAAAUGCCAACAAUAAGCCAAGAACAAAUU----UAUGCA-CUUAAUACACUGAA
.(((....((((((((.(((((((.((..(((((.......)))))...))(((......))).....)))))))..)))))))).----...)))-.............. ( -25.80)
>DroAna_CAF1 37652 105 + 1
UUGUUUGUAUUUGUUUAGGCUUAUGGCCAAGACGAUAAAAACGUCUCAAGCGCAGACAAAUGCCCAGAGAAAACAA-CUG--ACUGAGC-CUGACU-UGGCACAAU-CGAA
(((((((..((((....(((.....))).(((((.......)))))))))..))))))).................-.((--(.((.((-(.....-.))).)).)-)).. ( -27.00)
>DroPer_CAF1 37171 107 + 1
UUGUUUGUAUUUGUUUAGGCUUAUGGCCAAGACGAUAAAAACGUCUCGAGCGCCGACAAAUGGCCGGAGAAAGCAG-GCG--GAUGACGGCCGACUUUAGAGCCAU-CGAA
..((((....((((((.(((.....))).))))))...))))...(((((.((((.....)))))((..((((..(-((.--(....).)))..))))....)).)-))). ( -31.00)
>consensus
UUGUUUGUAUUUGUUUAGGCUUAUGGCCAAGACGAUAAAAACGUCUCAAGCGCAGACAAAUGCCCAGAGAAAACAA_GAG__AAUGACG_CCGACU_UAGAACAAU_CGAA
(((((((..((((....(((.....))).(((((.......)))))))))..))))))).................................................... (-18.24 = -18.22 +  -0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:26 2006